[Freesurfer] mris_convert reading surf.gii files?

[Westin, Karin]

External Email - Use Caution

Hi


I'm trying to create an .annot file from a label.gii file using an HCP 
fsavarage.surf.gii file (eg mris_convert --annot my_label.label.gii 
fsaverage_template.L.surf.gii lh.my_annot.annot). However I keep getting the 
error


** failed to open GIFTI XML file 
'fs_L-to-fs_LR_fsaverage.L_LR.spherical_std.164k_fs_L.surf.gii'

mrisReadGIFTIdanum: gifti_read_image() returned NULL

Is there a better way to read/open CIFTI files using mris_convert?

Best and thanks
Karin

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Re: [Freesurfer] consistency in recon-all parallel pipeline

[Douglas N. Greve]

Can you try it with -threads instead? We don't typically use -parallel

On 2/23/2024 2:44 PM, Horn, Mitchell Jacob wrote:


This is all with ‘recon-all -parallel’

Thanks,

Mitch

*From:*freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *Huang, Yujing

*Sent:* Friday, February 23, 2024 2:30 PM
*To:* Freesurfer support list 
*Subject:* Re: [Freesurfer] consistency in recon-all parallel pipeline

Do you run ‘recon-all -parallel’ or ‘recon-all –threads ’?

*From:*freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *Horn, Mitchell 
Jacob

*Sent:* Friday, February 23, 2024 12:28 PM
*To:* Freesurfer support list 
*Subject:* Re: [Freesurfer] consistency in recon-all parallel pipeline

Bottom line is that when I run any FreeSurfer version 7+ in parallel 
on COS8 I get different results each time.


Thanks,

Mitch

*From:*freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *Douglas N. Greve

*Sent:* Friday, February 23, 2024 11:03 AM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] consistency in recon-all parallel pipeline

So, is the bottom line that when you run 7.4.1 on COS8 in parallel 
that you get (slightly) different results each time?


On 2/2/2024 11:20 AM, Horn, Mitchell Jacob wrote:

Hi FS Devs,

I’m experiencing unreproducible thickness results when running any
7+ version with parallelization enabled. Running recon-all without
parallelization produces consistent thickness results. I’m running
this in AlmaLinux8 (a library-equivalent downstream OS to CentOS8).

I’m attaching a table (table1) of 12 recons with bert:

 1. 3 parallelized with CentOS8-compiled 7.4.1
 2. 3 non-parallelized with CentOS8-compiled 7.4.1
 3. 3 parallelized with CentOS7-compiled 7.4.1
 4. 3 non-parallelized with CentOS7-compiled 7.4.1

I suspected the downstream CentOS8 libm was the culprit (because
of testing I did this last 2023 summer). I ran 3 more recons
parallelized with the CentOS7-compiled 7.4.1, but before running
the recon-all command, set LD_PRELOAD to a copy of the CentOS7
libm libraries. The thickness results were then consistent, see
the second table below (table2). I could not run this experiment
on the CentOS8-compiled version, as that one is obviously not
backward compatible with CentOS7 libm.

As a quick test of the OS-dependency, I submitted 3 parallel
recons on MLSC with 7.3.3. Each reported different thickness. See
table 3 (table3).

I’m asking if you can please confirm whether running any 7.+
version with parallelization is generating reproducible results
for you in CentOS8 (or equivalent)?

P.S. - I tested 6.0 (CentOS6-compilation) with parallelization,
and the results were consistent.

Best,

Mitch

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