[prfanalyze-vista] Unrecognized variable name 'stimulus_diameter'.

[Gilles86]

Hey guys,

I'm trying some packages to fit synthesized data from prfsynth.

I created data using

docker run --rm -it \
    --platform linux/amd64 \
    -v "$script_dir/$json_file:/flywheel/v0/input/config.json" \
    -v "$basedir:/flywheel/v0/output" \
    garikoitz/prfsynth

With the json-file basically the default-config of prfsynth.

I then get the following error when I try to fit:

./fit_mrvista.sh verysmall
Running with identifier: verysmall
Using config file: /home/ubuntu/git/paper_braincoder/prfsynth/fit/mrvista/configs/prfanalyze-vista-verysmall.json
WARNING: Using temporary output directory: /flywheel/v0/output/BIDS/derivatives/prfanalyze-vista_temp001
[base/run.py] Using real data, not coming from prfsynthesize.
[base/run.py] This is the temp file with stim info:
/tmp/tmpzu447l.json
[base/run.py] This is the content:
{u'fieldofviewHorz': 20, 'isPRFSynthData': False}
------------------------------------------
Setting up environment variables
---
LD_LIBRARY_PATH is .:/opt/mcr/v95//runtime/glnxa64:/opt/mcr/v95//bin/glnxa64:/opt/mcr/v95//sys/os/glnxa64:/opt/mcr/v95//sys/opengl/lib/glnxa64
This is the config.json file being read: /running/out/options.json
These are the contents of the json file:

tmp =

  struct with fields:

               keepAllPoints: 0
              coarseDecimate: 2
          prfprepareAnalysis: '01'
    numberStimulusGridPoints: 50
                     detrend: 1
                     wsearch: 'coarse to fine'
                        grid: 0
                       model: 'one gaussian'
                         hrf: {0x1 cell}

================================================================================
/flywheel/v0/input/BIDS/sub-verysmall/ses-1/func/sub-verysmall_ses-1_task-prf_acq-normal_run-01_bold.nii.gz
/tmp/tmpzu447l.json
/flywheel/v0/input/BIDS/stimuli/sub-verysmall_ses-1_task-prf_apertures.nii.gz
/running/out/options.json
--------------------------------------------------------------------------------
This is the options file comming in:

allOptions =

  struct with fields:

    vista: [1x1 struct]
     aprf: [1x1 struct]
     afni: [1x1 struct]
      mlr: [1x1 struct]

Error using pmModelFit (line 128)
Unrecognized variable name 'stimulus_diameter'.

Error in prfanalyze_vista (line 96)

MATLAB:table:UnrecognizedVarName

real    0m15.149s
user    0m12.074s
sys     0m2.320s
<ERROR>      An error occurred during execution of the Matlab executable. Exiting!

Note that prfsynth/aprf, prfsynth/popeye, prfsynth/afni can all fit this data out-of-the-box.

Cheers,
Gilles

[garikoitz]

Please can you attach the config file? What version of the prfanalyze are you using? cheers, Gari

…

On Thu, Jan 30, 2025 at 10:29 AM Gilles de Hollander < ***@***.***> wrote: Hey guys, I'm trying some packages to fit synthesized data from prfsynth. I created data using docker run --rm -it \ --platform linux/amd64 \ -v "$script_dir/$json_file:/flywheel/v0/input/config.json" \ -v "$basedir:/flywheel/v0/output" \ garikoitz/prfsynth With the json-file basically the default-config of prfsynth. I then get the following error when I try to fit: ./fit_mrvista.sh verysmall Running with identifier: verysmall Using config file: /home/ubuntu/git/paper_braincoder/prfsynth/fit/mrvista/configs/prfanalyze-vista-verysmall.json WARNING: Using temporary output directory: /flywheel/v0/output/BIDS/derivatives/prfanalyze-vista_temp001 [base/run.py] Using real data, not coming from prfsynthesize. [base/run.py] This is the temp file with stim info: /tmp/tmpzu447l.json [base/run.py] This is the content: {u'fieldofviewHorz': 20, 'isPRFSynthData': False} ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/opt/mcr/v95//runtime/glnxa64:/opt/mcr/v95//bin/glnxa64:/opt/mcr/v95//sys/os/glnxa64:/opt/mcr/v95//sys/opengl/lib/glnxa64 This is the config.json file being read: /running/out/options.json These are the contents of the json file: tmp = struct with fields: keepAllPoints: 0 coarseDecimate: 2 prfprepareAnalysis: '01' numberStimulusGridPoints: 50 detrend: 1 wsearch: 'coarse to fine' grid: 0 model: 'one gaussian' hrf: {0x1 cell} ================================================================================ /flywheel/v0/input/BIDS/sub-verysmall/ses-1/func/sub-verysmall_ses-1_task-prf_acq-normal_run-01_bold.nii.gz /tmp/tmpzu447l.json /flywheel/v0/input/BIDS/stimuli/sub-verysmall_ses-1_task-prf_apertures.nii.gz /running/out/options.json -------------------------------------------------------------------------------- This is the options file comming in: allOptions = struct with fields: vista: [1x1 struct] aprf: [1x1 struct] afni: [1x1 struct] mlr: [1x1 struct] Error using pmModelFit (line 128) Unrecognized variable name 'stimulus_diameter'. Error in prfanalyze_vista (line 96) MATLAB:table:UnrecognizedVarName real 0m15.149s user 0m12.074s sys 0m2.320s <ERROR> An error occurred during execution of the Matlab executable. Exiting! Note that prfsynth/aprf, prfsynth/popeye, prfsynth/afni can all fit this data out-of-the-box. Cheers, Gilles — Reply to this email directly, view it on GitHub <#97>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABCZAV7ZK7LB2M4UV7QVUMD2NHWIXAVCNFSM6AAAAABWEZDWYSVHI2DSMVQWIX3LMV43ASLTON2WKOZSHAZDAMZRHAZTIOA> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[Gilles86]

Here you go.

prfsynth-verysmall.json

prfanalyze-vista-verysmall.json

[garikoitz]

can you try adding stimulus_diameter to the prfanalyze config? can you download the default for that gear? are you using prfanalyze-vista:2.3.0_3.1.2? thanks!

…

On Thu, Jan 30, 2025 at 10:53 AM Gilles de Hollander < ***@***.***> wrote: Here you go. prfsynth-verysmall.json <https://github.com/user-attachments/files/18600546/prfsynth-verysmall.json> prfanalyze-vista-verysmall.json <https://github.com/user-attachments/files/18600559/prfanalyze-vista-verysmall.json> — Reply to this email directly, view it on GitHub <#97 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABCZAV2T6D3BFSVHLJ46VI32NHZAPAVCNFSM6AAAAABWEZDWYSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMMRUGAYTGNJVGY> . You are receiving this because you commented.Message ID: ***@***.***>

[Gilles86]

Hey @garikoitz ,

Yes. That was the issue. When I use this config:

{
    "subjectName"    : "verysmall",
    "sessionName"    : "1",
    "solver"         : "vista",
    "tasks"          : "[all]",
    "isPRFSynthData" : true,
    "options": {
    	"prfprepareAnalysis" : "01",
        "hrf": [],
        "model"              : "one gaussian",
        "grid"               :  false,
        "wsearch"            : "coarse to fine",
        "detrend"            : 1,
        "keepAllPoints"      : false,
        "numberStimulusGridPoints": 50,
        "coarseDecimate": 2
    },
    "stimulus": {
    	"fieldofviewHorz":20,
        "stimulus_diameter":20
    }
}

That works!

Note that the stimulus_diameter is missing from your default config file

One more note: When I try to run your package as a singularity container, I get the following error:

CONFIG_FILE=$PWD/configs/prfanalyze-vista-${IDENTIFIER}.json
OUTPUT_DIR=/shares/zne.uzh/gdehol/ds-prfsynth
SIF_IMAGE=/shares/zne.uzh/containers/prfanalyze-vista.sif

echo "Running with identifier: $IDENTIFIER"
echo "Using config file: $CONFIG_FILE"

# Run Singularity with writable-tmpfs
singularity exec --cleanenv --writable-tmpfs \
    --bind "$OUTPUT_DIR:/flywheel/v0/input" \
    --bind "$OUTPUT_DIR:/flywheel/v0/output" \
    --bind $CONFIG_FILE:/flywheel/v0/input/config.json \
    "$SIF_IMAGE" \
    /flywheel/v0/run.sh
Running with identifier: verysmall
Using config file: /home/gdehol/git/paper_braincoder/prfsynth/fit/mrvista/configs/prfanalyze-vista-verysmall.json
INFO:    Mounting image with FUSE.
Preparing solver "prfanalyze-vista":
[base/run.py] Using synthetic data coming from prfsynthesize.
  Subject: verysmall
  Session: 1
  Options: {'prfprepareAnalysis': '01', 'hrf': [], 'model': 'one gaussian', 'grid': False, 'wsearch': 'coarse to fine', 'detrend': 1, 'keepAllPoints': False, 'numberStimulusGridPoints': 50, 'coarseDecimate': 2}
WARNING: Using temporary output directory: /flywheel/v0/output/BIDS/derivatives/prfanalyze-vista_temp006
Output BIDS directory: /flywheel/v0/output/BIDS/derivatives/prfanalyze-vista_temp006/sub-verysmall/ses-1
Beginning os.wait() for /solve.sh, run=01 (child pid is 3991966)
Failed to exec /solve.sh script!
No estimates.json file found.

Again, it works fine with afni and popeye (but not prfanalyze-aprf!)

This makes it impossible to run this stuff on our cluster. Is this a known issue? Do you want me to open a new one for that?

[garikoitz]

weird! will test, we use Singularity too

…

On Thu, Jan 30, 2025 at 11:20 AM Gilles de Hollander < ***@***.***> wrote: Hey @garikoitz <https://github.com/garikoitz> , Yes. That was the issue. When I use this config: { "subjectName" : "verysmall", "sessionName" : "1", "solver" : "vista", "tasks" : "[all]", "isPRFSynthData" : true, "options": { "prfprepareAnalysis" : "01", "hrf": [], "model" : "one gaussian", "grid" : false, "wsearch" : "coarse to fine", "detrend" : 1, "keepAllPoints" : false, "numberStimulusGridPoints": 50, "coarseDecimate": 2 }, "stimulus": { "fieldofviewHorz":20, "stimulus_diameter":20 } } That works! Note that the stimulus_diameter is missing from your default config file <https://github.com/vistalab/PRFmodel/blob/51ab893548dac1e914ba93da7580e3fae020010b/gear/prfanalyze/vista/default_config.json#L18> One more note: When I try to run your package as a singularity container, I get the following error: CONFIG_FILE=$PWD/configs/prfanalyze-vista-${IDENTIFIER}.json OUTPUT_DIR=/shares/zne.uzh/gdehol/ds-prfsynth SIF_IMAGE=/shares/zne.uzh/containers/prfanalyze-vista.sif echo "Running with identifier: $IDENTIFIER" echo "Using config file: $CONFIG_FILE" # Run Singularity with writable-tmpfs singularity exec --cleanenv --writable-tmpfs \ --bind "$OUTPUT_DIR:/flywheel/v0/input" \ --bind "$OUTPUT_DIR:/flywheel/v0/output" \ --bind $CONFIG_FILE:/flywheel/v0/input/config.json \ "$SIF_IMAGE" \ /flywheel/v0/run.sh Running with identifier: verysmall Using config file: /home/gdehol/git/paper_braincoder/prfsynth/fit/mrvista/configs/prfanalyze-vista-verysmall.json INFO: Mounting image with FUSE. Preparing solver "prfanalyze-vista": [base/run.py] Using synthetic data coming from prfsynthesize. Subject: verysmall Session: 1 Options: {'prfprepareAnalysis': '01', 'hrf': [], 'model': 'one gaussian', 'grid': False, 'wsearch': 'coarse to fine', 'detrend': 1, 'keepAllPoints': False, 'numberStimulusGridPoints': 50, 'coarseDecimate': 2} WARNING: Using temporary output directory: /flywheel/v0/output/BIDS/derivatives/prfanalyze-vista_temp006 Output BIDS directory: /flywheel/v0/output/BIDS/derivatives/prfanalyze-vista_temp006/sub-verysmall/ses-1 Beginning os.wait() for /solve.sh, run=01 (child pid is 3991966) Failed to exec /solve.sh script! No estimates.json file found. Again, it works fine with afni and popeye (but not prfanalyze-aprf!) This makes it impossible to run this stuff on our cluster. Is this a known issue? Do you want me to open a new one for that? — Reply to this email directly, view it on GitHub <#97 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABCZAV6NJPSBOXNRSNCI7ST2NH4FVAVCNFSM6AAAAABWEZDWYSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMMRUGA3TMMBUGU> . You are receiving this because you were mentioned.Message ID: ***@***.***>