Re: [Freesurfer] mris_preproc error: cannot allocate memory

Wassima Sent: Tuesday, August 1, 2023 4:49 PM To: Freesurfer support list Subject: Re: [Freesurfer] mris_preproc error: cannot allocate memory External Email - Use Caution Hello M.Yujing, I’m using the HCP-A cohort (Human Connectome Project – Aging), where the structural MRIs were

Re: [Freesurfer] mris_preproc error: cannot allocate memory

wondering how you created /media/sf_T1/freesurfer_results/HCA9679715_V1_MR/surf/lh.sphere.reg? Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of MANSSOUR Wassima Sent: Tuesday, August 1, 2023 2:52 PM To: Freesurfer support list Subject: Re: [Freesurfer] mris_preproc error

Re: [Freesurfer] mris_preproc error: cannot allocate memory

External Email - Use Caution That should be enough RAM. What is your command line? Can you send the log file? On 8/1/2023 7:52 AM, MANSSOUR Wassima wrote: External Email - Use Caution Hello FreeSurfer Developers, I'm conducting the *Surface Based Group Analysis* 

Re: [Freesurfer] mris_preproc read error

Graduate Program University of California, San Diego From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve Sent: Thursday, June 9, 2022 1:27 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_preproc read error It looks

Re: [Freesurfer] mris_preproc read error

, June 3, 2022 10:37 AM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] mris_preproc read error External Email - Use Caution Dear FreeSurfer team, I reran -qcache for sub-101 (also, I had specified -qcache processing for all subjects during initial recon-all so it /should/ have

Re: [Freesurfer] mris_preproc read error

: [Freesurfer] mris_preproc read error External Email - Use Caution Dear FreeSurfer team, I reran -qcache for sub-101 (also, I had specified -qcache processing for all subjects during initial recon-all so it should have already occurred), and it exited with errors. Below is the output from

Re: [Freesurfer] mris_preproc read error

From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve Sent: Friday, June 3, 2022 10:03 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_preproc read error Try running recon-all -s subject -qcache for that subject On 6/2/2022

Re: [Freesurfer] mris_preproc read error

Try running recon-all -s subject -qcache for that subject On 6/2/2022 7:55 PM, Joanna L Eckhardt wrote: External Email - Use Caution Dear FreeSurfer Help Team, I am working through the FreeSurfer tutorial on cannabis using Ubuntu VM on windows (FS version 7.1.1). I am on the group

[Freesurfer] mris_preproc read error

External Email - Use Caution Dear FreeSurfer Help Team, I am working through the FreeSurfer tutorial on cannabis using Ubuntu VM on windows (FS version 7.1.1). I am on the group analysis portion of the tutorial attempting to run mris_preproc. However, I am receiving the

Re: [Freesurfer] mris_preproc error: no source hemi specified

Did you specify a hemi? If you run it with --help it will give you docs. You can also  find them on line. You should also send the command line On 2/17/2022 9:23 AM, Koustav Chatterjee wrote: External Email - Use Caution Dear FreeSurfer experts, I need your help. I am trying to run

[Freesurfer] mris_preproc error: no source hemi specified

External Email - Use Caution Dear FreeSurfer experts, I need your help. I am trying to run mris_preproc --fsgd in order to see the effect of cortical volume on velocity, accounting for the effects of eTIV in the analysis. My .fsgd file looks like GroupDescriptorFile 1 Title

Re: [Freesurfer] mris_preproc label file not found

External Email - Use Caution Thank you Tim, the explanation and screenshot helped indeed. Diana El mar., 9 jun. 2020 a las 10:07, Tim Schäfer () escribió: > External Email - Use Caution > > These are different versions of the fsaverage template, but with reduced > vertex

Re: [Freesurfer] mris_preproc label file not found

External Email - Use Caution These are different versions of the fsaverage template, but with reduced vertex count (mesh resolution). The default fsaverage subject has the highest resolution, and it gets lower for fsaverage6, 5, ... and so on. Put another way, fsaverage3 is

Re: [Freesurfer] mris_preproc label file not found

External Email - Use Caution Tim, my bad I do have it in the installation folder: ls -l $FREESURFER_HOME/subjects/fsaverage/label/lh.cortex.label -rwxrwxr-x 1 8481 1590 6117569 ago 14 2007 /usr/local/freesurfer/subjects/fsaverage/label/lh.cortex.label Please, could you explain

Re: [Freesurfer] mris_preproc label file not found

External Email - Use Caution Hm, if you do not have the file in $FREESURFER_HOME/subjects/fsaverage/label/, your FreeSurfer installation is incomplete I guess. The file should definitely come with the software. What is the output of: ls -l

Re: [Freesurfer] mris_preproc label file not found

External Email - Use Caution Dear Tim, Thank you for your fast response. I did not have it in my fsaverage directory but I did find it in "tutorial_data_20190918_1558/buckner_data/tutorial_subjs/fsaverage", would it be correct to use that one or should I create a new one? If I

Re: [Freesurfer] mris_preproc label file not found

External Email - Use Caution I think all you need to do is copy (or symlink) fsaverage to your data directory, the label file is in there already. e.g.: cp -r $FREESURFER_HOME/subjects/fsaverage /home/neuroimagen/AnalisisLongitudinalLMM Best, Tim > On June 8, 2020 at 7:29

[Freesurfer] mris_preproc label file not found

External Email - Use Caution Dear experts, I am preparing my data for longitudinal statistical analysis following the steps in https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalStatistics#LinearMixedEffectsModel. I try running the following comand : mris_preproc

Re: [Freesurfer] mris_preproc not running

> > Sara Sims > > > > Graduate Research Fellow > > > > University of Alabama at Birmingham > > > > Department of Psychology > > > > 205-975-4060 > > > > sno...@uab.edu >

Re: [Freesurfer] mris_preproc not running

a Sims > > Graduate Research Fellow > > University of Alabama at Birmingham > > Department of Psychology > > 205-975-4060 > > sno...@uab.edu > > *From: * on behalf of "Greve, > Douglas N.,Ph.D."

Re: [Freesurfer] mris_preproc not running

> Sara Sims > > Graduate Research Fellow > > University of Alabama at Birmingham > > Department of Psychology > > 205-975-4060 > > sno...@uab.edu > > *From: * on behalf of "Greve, > Douglas N.,Ph.D." > *Reply-To: *Freesurfer support lis

Re: [Freesurfer] mris_preproc not running

Department of Psychology 205-975-4060 sno...@uab.edu From: on behalf of "Greve, Douglas N.,Ph.D." Reply-To: Freesurfer support list Date: Saturday, March 30, 2019 at 6:06 PM To: "freesurfer@nmr.mgh.harvard.edu" Subject: Re: [Freesurfer] mris_preproc not running Hi Sara, can yo

Re: [Freesurfer] mris_preproc not running

vard.edu> on behalf of "Greve, > > Douglas N.,Ph.D." <mailto:dgr...@mgh.harvard.edu> > > *Reply-To: *Freesurfer support list <mailto:freesurfer@nmr.mgh.harvard.edu> > > *Date: *Monday, March 18, 2019 at 10:24 AM > >

Re: [Freesurfer] mris_preproc not running

> > > sno...@uab.edu > > > > *From: * on behalf of "Greve, > > Douglas N.,Ph.D." > > *Reply-To: *Freesurfer support list > > *Date: *Monday, March 18, 2019 at 10:24 AM > > *To: *"freesurfer@nmr.mgh.harvard.ed

Re: [Freesurfer] mris_preproc not running

Alabama at Birmingham > > Department of Psychology > > 205-975-4060 > > sno...@uab.edu > > *From: * on behalf of "Greve, > Douglas N.,Ph.D." > *Reply-To: *Freesurfer support list > *Date: *Monday, Mar

Re: [Freesurfer] mris_preproc not running

uot; > *Reply-To: *Freesurfer support list > *Date: *Monday, March 18, 2019 at 10:24 AM > *To: *"freesurfer@nmr.mgh.harvard.edu" > *Subject: *Re: [Freesurfer] mris_preproc not running > > > can you send the terminal output? I realize it might be quite big. You > c

Re: [Freesurfer] mris_preproc not running

of "Greve, Douglas N.,Ph.D." Reply-To: Freesurfer support list Date: Monday, March 18, 2019 at 10:24 AM To: "freesurfer@nmr.mgh.harvard.edu" Subject: Re: [Freesurfer] mris_preproc not running can you send the terminal output? I realize it might be quite big. You can ftp it to

Re: [Freesurfer] mris_preproc not running

can you send the terminal output? I realize it might be quite big. You can ftp it to here: /autofs/space/nihilus_001/CICS/ACRsoftware/ACRcurrent On 3/18/19 11:12 AM, Sims, Sara A (Campus) wrote: External Email - Use Caution Hello! I have 786 subjects that I am trying to do a paired

[Freesurfer] mris_preproc not running

External Email - Use Caution Hello! I have 786 subjects that I am trying to do a paired difference analysis using mri_glm. I am getting stuck at the mris_preproc stage. I have tried running it on a handful of subjects and it works wonderfully. However, when I run it on all the

Re: [Freesurfer] mris_preproc error: dimension mismatch

, 2019 9:22 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_preproc error: dimension mismatch If you have a volume and a registration file, you can run mris_preproc with the --iv option. Eg, something like mris_preproc --fsgd abc.fsgd --target fsaverage --hemi lh \ * --out abc

Re: [Freesurfer] mris_preproc error: dimension mismatch

- > *From:* freesurfer-boun...@nmr.mgh.harvard.edu > on behalf of Greve, Douglas > N.,Ph.D. > *Sent:* Friday, February 15, 2019 8:26 AM > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* Re: [Freesurfer] mris_preproc error: dimension mismatch > The subject s

Re: [Freesurfer] mris_preproc error: dimension mismatch

, 2019 8:26 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_preproc error: dimension mismatch The subject surface probably changed since the last time you ran qcache and now has a different number of vertices. Try re-running qcache for those subjects. On 2/15/19 2:58 AM, Peters

Re: [Freesurfer] mris_preproc calling on incorrect target surface

The commands I use for the mri_preproc are below, with the sections I > am referring to highlighted in bold. > > ebunting@img-140:.../MRI_data/freesurfer$ mris_preproc --fsgd > PDonly_Liu_EB.fsgd \ > > *> --target avgsubject.Patients_EB \* > > > --hemi lh \ > > &

Re: [Freesurfer] mris_preproc error: dimension mismatch

The subject surface probably changed since the last time you ran qcache and now has a different number of vertices. Try re-running qcache for those subjects. On 2/15/19 2:58 AM, Peters, Douglas G wrote: External Email - Use Caution Hi Everyone, I'm trying to prepare my Cerebral blood

[Freesurfer] mris_preproc error: dimension mismatch

External Email - Use Caution Hi Everyone, I'm trying to prepare my Cerebral blood flow surface data for mri_glmfit group analysis (qdec doesn't allow you to choose your own subject surface files to analyze, so I figured mri_glmfit is my only option). Quick summary of what I

[Freesurfer] mris_preproc calling on incorrect target surface

for the mri_preproc are below, with the sections I am referring to highlighted in bold. ebunting@img-140:.../MRI_data/freesurfer$ mris_preproc --fsgd PDonly_Liu_EB.fsgd \ > --target avgsubject.Patients_EB \ > --hemi lh \ > --meas thickness \ > --out lh.PDonly_Liu_AvgSubjectPatients_EB.thic

Re: [Freesurfer] mris_preproc paired diff outputs 0 values

December 3, 2018 at 10:56 AM > *To: *Freesurfer support list > *Subject: *[Freesurfer] mris_preproc paired diff outputs 0 values > > *External Email - Use Caution * > > Hello, > > I am trying to do a paired difference analysis of two runs of > probtrackx (

Re: [Freesurfer] mris_preproc paired diff outputs 0 values

Subject: [Freesurfer] mris_preproc paired diff outputs 0 values External Email - Use Caution Hello, I am trying to do a paired difference analysis of two runs of probtrackx (I have already put them on the surface). The two conditions are “central” and “far” for each subject. I have already

[Freesurfer] mris_preproc paired diff outputs 0 values

External Email - Use Caution Hello, I am trying to do a paired difference analysis of two runs of probtrackx (I have already put them on the surface). The two conditions are “central” and “far” for each subject. I have already checked the individual subjects data and it does

[Freesurfer] mris_preproc paired diff outputs 0 values

External Email - Use Caution Hello, I am trying to do a paired difference analysis of two runs of probtrackx (I have already put them on the surface). The two conditions are “central” and “far” for each subject. I have already checked the individual subjects data and it does

Re: [Freesurfer] mris_preproc error

you will also need to recreate lh.MS073_R01_05-t2star_05iso_corr_disco_r0.8_depth0.5_fwhm3.mgh On 5/21/18 12:45 PM, Barletta, Valeria wrote: > Hi Freesurfers, > I sent this help request some days ago but had some problems in receiving the > reply because of mailing list subscription issues...

[Freesurfer] mris_preproc error

Hi Freesurfers, I sent this help request some days ago but had some problems in receiving the reply because of mailing list subscription issues... Sorry for submitting this request again: I used the command mris_preproc to have all the surfaces of my cohort concatenated in fs average and I

Re: [Freesurfer] mris_preproc error

You probably need to regenerate this file: /autofs/space/alicudi_002/users/mscat/users/gabriel/R01_Automatic/MS073_R01_05/Bay8_3T/fs/MS073_R01_05/surf/overlay/lh.MS073_R01_05-t2star_05iso_corr_disco_r0.8_depth0.5_fwhm3.mgh On 5/11/18 2:39 PM, Barletta, Valeria wrote: > Hi Freesurfers, > I used

[Freesurfer] mris_preproc error

Hi Freesurfers, I used the command mris_preproc to have all the surfaces of my cohort concatenated in fs average and I obtained this error message from several of my subjects: #@# 3/11 MS073_R01_05/Bay8_3T/fs/MS073_R01_05 Fri May 11 14:24:58 EDT 2018 -- ---

Re: [Freesurfer] mris_preproc srcsurfreg Freesurfer 6.0

Thanks you anyway, Douglas ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe

Re: [Freesurfer] mris_preproc srcsurfreg Freesurfer 6.0

Thank you for the insight; that is very interesting. I'm performing tests of continuous independent variables over a single sample of normally developing children (ages uniformly distributed from 8

Re: [Freesurfer] mris_preproc srcsurfreg Freesurfer 6.0

It might capture specific anatomical features that are unique to your data set. It can be tricky though as you need to make sure to include an equal mix of all your groups. Eg, if you have 20 ADs and 10 controls, you'd need to make an atlas with 10 ADs and 10 controls. On 11/08/2017 03:57 PM,

Re: [Freesurfer] mris_preproc srcsurfreg Freesurfer 6.0

no, sorry On 11/09/2017 03:50 AM, M del Mar Velasco wrote: > > Thanks you for your reply. > > I have used surfreg script and now it runs correctly. However, my > subject list is very long, I have 100 subjects and running surfreg > with all subject takes 13 hours (using all my cpus in a

Re: [Freesurfer] mris_preproc srcsurfreg Freesurfer 6.0

Thanks you for your reply. I have used surfreg script and now it runs correctly. However, my subject list is very long, I have 100 subjects and running surfreg with all subject takes 13 hours (using all my cpus in a parallel way). Is there any option to reduce this long time? Any cuda file?

Re: [Freesurfer] mris_preproc srcsurfreg Freesurfer 6.0

Dear Doug, Are there reasons why registering to my_subject_average (template defined from, say, average in a cross-sectional sample) can be better than registering to fsaverage? Thank you. Best, Chintan ___ Freesurfer mailing list

Re: [Freesurfer] mris_preproc srcsurfreg Freesurfer 6.0

The way that mris_preproc used to work was confusing. It made it look like you were actually sampling to my_subject_average. In reality, it was only using my_subject_average to perform smoothing -- the entire analysis was done in fsaverage space. To clarify this, I required that there by a new

[Freesurfer] mris_preproc srcsurfreg Freesurfer 6.0

Dear FreeSurfer experts, I am using mris_preproc command with following options: mris_preproc --s s_001 --s s_002 --s s_003 --target my_subject_average --hemi lh --meas my_input_surf.mgh --out /my_output_path/output_file I observe mris_preproc uses mri_surf2surf. My question is related

Re: [Freesurfer] mris_preproc version 6

-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Thursday, February 16, 2017 1:32 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_preproc version 6 here you go https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_preproc On 02/16

Re: [Freesurfer] mris_preproc version 6

here you go https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_preproc On 02/16/2017 01:18 PM, Fotiadis, Panagiotis wrote: > Hi Doug and Bruce, > > I was wondering whether you know where I can download the version 6 > mris_preproc! > > Thanks in advance, > Panos > > Panagiotis Fotiadis >

[Freesurfer] mris_preproc version 6

Hi Doug and Bruce, I was wondering whether you know where I can download the version 6 mris_preproc! Thanks in advance, Panos Panagiotis Fotiadis Research Technologist II J. P. Kistler Stroke Research Center Massachusetts General Hospital 175 Cambridge Street, Suite 300 Boston, MA, 02114 T:

Re: [Freesurfer] mris_preproc

Thank you very much Doug! -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Friday, November 4, 2016 12:14 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_preproc

Re: [Freesurfer] mris_preproc

rfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve > Sent: Friday, November 4, 2016 12:09 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] mris_preproc > > Do you have a question about the image? > >

Re: [Freesurfer] mris_preproc

e- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve > Sent: Friday, November 4, 2016 10:29 AM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] mris_preproc > > > > On 11/04/201

Re: [Freesurfer] mris_preproc

Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Friday, November 4, 2016 12:09 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_preproc Do you have a question about the image

Re: [Freesurfer] mris_preproc

On 11/04/2016 07:25 AM, Alshikho, Mohamad J. wrote: > > Dear FS experts, > > I ran surface based analysis using PET maps, and the pipeline > reported, in FS list, by multiple colleagues as the following: > > ·spmregister --s subj --mov pet.nii --reg reg.dat --out pet_t1.mgh > > ·mris_preproc

[Freesurfer] mris_preproc

Dear FS experts, I ran surface based analysis using PET maps, and the pipeline reported, in FS list, by multiple colleagues as the following: * spmregister --s subj --mov pet.nii --reg reg.dat --out pet_t1.mgh * mris_preproc --target fsaverage --hemi lh --iv

Re: [Freesurfer] mris_preproc subject-volume mismatch

@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_preproc subject-volume mismatch Ah, the problem is with using an lta with 5.3 mris_preproc. I've put version 6 mris_preproc here ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_preproc try that and see if it works. Alternatively, you

Re: [Freesurfer] mris_preproc subject-volume mismatch

t; Sent: Wednesday, July 06, 2016 1:54 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] mris_preproc subject-volume mismatch > > It must be that one of the ces files has multiple frames. Try running > mri_info --nframes ces.nii.gz > on all of the ces file

Re: [Freesurfer] mris_preproc subject-volume mismatch

To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_preproc subject-volume mismatch It must be that one of the ces files has multiple frames. Try running mri_info --nframes ces.nii.gz on all of the ces files to see how many frames are in each On 07/06/2016 01:39 PM, Raney, Talia L. wrote

Re: [Freesurfer] mris_preproc subject-volume mismatch

rvard.edu] on behalf of Douglas N Greve > [gr...@nmr.mgh.harvard.edu] > Sent: Wednesday, July 06, 2016 1:19 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] mris_preproc subject-volume mismatch > > can you send the terminal output? > > On 07/06/2016

Re: [Freesurfer] mris_preproc subject-volume mismatch

[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Wednesday, July 06, 2016 1:19 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_preproc subject-volume mismatch can you send the terminal output? On 07/06/2016 11:32 AM, Raney

Re: [Freesurfer] mris_preproc subject-volume mismatch

can you send the terminal output? On 07/06/2016 11:32 AM, Raney, Talia L. wrote: > Hi FreeSurfer users, > I'm trying to use mri-preproc to do a group fMRI analysis(based on the > tutorial). However, I keep getting an error that the number of input volumes > does not equal number of subjects. It

[Freesurfer] mris_preproc subject-volume mismatch

Hi FreeSurfer users, I'm trying to use mri-preproc to do a group fMRI analysis(based on the tutorial). However, I keep getting an error that the number of input volumes does not equal number of subjects. It seems one volume is counted as 4 subjects. I'm wondering what the command determines to

Re: [Freesurfer] mris_preproc - srcsubjreg

> From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve > [gr...@nmr.mgh.harvard.edu] > Sent: Tuesday, May 31, 2016 12:47 > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] mris_preproc -

Re: [Freesurfer] mris_preproc - srcsubjreg

.harvard.edu Subject: Re: [Freesurfer] mris_preproc - srcsubjreg Sorry for the delay. This is because sphere.reg only applies to fsaverage. Previously, the specification of a different target would only influence smoothing done as part of mris_preproc; the registration would still

Re: [Freesurfer] mris_preproc - srcsubjreg

Sorry for the delay. This is because sphere.reg only applies to fsaverage. Previously, the specification of a different target would only influence smoothing done as part of mris_preproc; the registration would still be done to fsaverage. This is probably not the intent of people who are

Re: [Freesurfer] mris_preproc - srcsubjreg

t; Johanna [smakar...@mgh.harvard.edu] > Sent: Tuesday, May 24, 2016 16:23 > To: Freesurfer support list > Subject: [Freesurfer] mris_preproc - srcsubjreg > > Hi Doug, I¹m curious why the newer mris_preproc does not use sphere.reg as > the default srcsurfreg when the target is not fsaverage

Re: [Freesurfer] mris_preproc - srcsubjreg

list Subject: [Freesurfer] mris_preproc - srcsubjreg Hi Doug, I¹m curious why the newer mris_preproc does not use sphere.reg as the default srcsurfreg when the target is not fsaverage - see below Thanks for any info! (not urgent) On 2016-5-24, 11:30, "Z K" <zkauf...@nmr.mgh.harva

[Freesurfer] mris_preproc - srcsubjreg

Hi Doug, I¹m curious why the newer mris_preproc does not use sphere.reg as the default srcsurfreg when the target is not fsaverage - see below Thanks for any info! (not urgent) On 2016-5-24, 11:30, "Z K" wrote: >Good question, and I dont know the answer.

[Freesurfer] mris_preproc on zipped data

Hi, I have a large amount of data (FS scanworkups) where all the files within every subject's directory are zipped. Is there a way to run mris_preproc on zipped data? For instance, mris_preproc crashes because it can't find lh.thickness unless I unzip it Thank you! sincerely yours,

Re: [Freesurfer] mris_preproc on zipped data

no, sorry On 01/28/2016 11:11 AM, Lars M. Rimol wrote: > Hi, > > I have a large amount of data (FS scanworkups) where all the files within > every subject's directory are zipped. Is there a way to run mris_preproc on > zipped data? > For instance, mris_preproc crashes because it can't find

Re: [Freesurfer] mris_preproc -iv option

It samples halfway between the white and pial On 8/13/15 6:52 AM, Silas wrote: Dear Freesurfer team, How does mris_preproc map volume data onto the surface when using the -ivoption? Is an average between the white and pial boundaries taken, orare only the voxels taken into account that

[Freesurfer] mris_preproc -iv option

Dear Freesurfer team, How does mris_preproc map volume data onto the surface when using the -iv option? Is an average between the white and pial boundaries taken, or are only the voxels taken into account that intersect with one of the two surfaces (and if yes, with which surface)?

Re: [Freesurfer] mris_preproc output file PET data

Hi Alex, mris_preproc produces a stack images (27 in the first case and 16 in the 2nd case). For some reason the first two images are the same in both stacks. This is the way that you have run the program because both calls to mris_preproc use NNC0035_pet_lh.mgh and NNC0045_pet_lh.mgh as the

Re: [Freesurfer] mris_preproc skips subjects

Can you send your fsgd file? On 02/21/2015 08:42 AM, Anders Hougaard wrote: Dear Freesurfers, Sorry for this newbie question: I'm preparing my data for a group analysis using mris_preproc: mris_preproc --fsgd nocov.fsgd --target fsaverage --hemi lh --meas thickness --out

Re: [Freesurfer] mris_preproc skips subjects

Hi again, I'm still totally stuck here. Any idea what the problem might be? I tried running mris_preproc with the --s option instead of --fsgd and this apparently works for all subjects that I tried so far. Now, using --fsgd, mris_preproc only processes the first subject in group 2?! All the

[Freesurfer] mris_preproc skips subjects

Dear Freesurfers, Sorry for this newbie question: I'm preparing my data for a group analysis using mris_preproc: mris_preproc --fsgd nocov.fsgd --target fsaverage --hemi lh --meas thickness --out lh.nocov.thickness.00.mgh I have 120 subjects in total and my FSGD file simply looks like this

[Freesurfer] mris_preproc error

Hi All, I am getting a consistent error when I try to run mris_preproc - I'm baffled as I've used all of my scripts and fsgd files before. There are 2 groups with 3 covariates but I keep getting this error: mris_preproc --fsgd fsgd/HRR60.fsgd --cache-in thickness.fwhm10.fsaverage --target

Re: [Freesurfer] mris_preproc error

Can you run it with --debug as the first argument and send the terminal output? doug On 11/05/2014 04:21 PM, Cooke, Gillian wrote: Hi All, I am getting a consistent error when I try to run mris_preproc - I'm baffled as I've used all of my scripts and fsgd files before. There are 2

Re: [Freesurfer] mris_preproc error

, November 05, 2014 4:26 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_preproc error Can you run it with --debug as the first argument and send the terminal output? doug On 11/05/2014 04:21 PM, Cooke, Gillian wrote: Hi All, I am getting a consistent error when I try to run

Re: [Freesurfer] mris_preproc error

[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Wednesday, November 05, 2014 4:26 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_preproc error Can you run it with --debug as the first argument and send

Re: [Freesurfer] mris_preproc error

: [Freesurfer] mris_preproc error run it like this mris_preproc --debug --fsgd fsgd/HRR60.fsgd ... doug On 11/05/2014 05:32 PM, Cooke, Gillian wrote: Unfortunately I'm getting this error in the terminal: bash: --debug: command not found From: freesurfer

Re: [Freesurfer] mris_preproc error

From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Wednesday, November 05, 2014 4:41 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_preproc error run

Re: [Freesurfer] mris_preproc error

To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_preproc error Hmm, still not sure what's up. Can you attach your fsgd file to an email? doug On 11/05/2014 05:48 PM, Cooke, Gillian wrote: Thanks Doug - this is what it produces: out mris_preproc/lh.HRR60.thickness.10.mgh set echo = 1

Re: [Freesurfer] mris_preproc error

-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Wednesday, November 05, 2014 5:10 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_preproc error Hmm, still not sure what's up. Can you attach

[Freesurfer] mris_preproc patch download

Hello list, I'm working with FS 5.0 and I'll be using either qdec or mri_glmfit for whole brain analysis. The link http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi#Installation takes me to ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/xhemi/mris_preproc where a script appears. I

Re: [Freesurfer] mris_preproc patch download

download the file and copy it into $FREESURFER_HOME/bin and make it executable (make a backup first) On 03/27/2014 09:37 AM, _andre...@sapo.pt wrote: Hello list, I'm working with FS 5.0 and I'll be using either qdec or mri_glmfit for whole brain analysis. The link

Re: [Freesurfer] mris_preproc patch download

Hi Doug, I had to Save file as... So, that was the download... Backup made and mris_preproc replaced by the new one. Thank you! Andreia Quoting Douglas N Greve gr...@nmr.mgh.harvard.edu: download the file and copy it into $FREESURFER_HOME/bin and make it executable (make a backup first)

[Freesurfer] mris_preproc patch

Dear Doug, I would need the mris_preproc patch, however the link provided (ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_preproc) is not working. Is there another way of getting the patch (rather than downloading the new version of FreeSurfer)? Best wishes, Nenad

Re: [Freesurfer] mris_preproc patch

you can get it from this page. You don't need the other files unless you are doing the interhemispheric analysis http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi On 03/21/2014 04:41 AM, N. Medic wrote: Dear Doug, I would need the mris_preproc patch, however the link provided

[Freesurfer] mris_preproc, mri_surf2surf and lme_mass_vw

Hello Freesurfer experts, The lme_mass_vw script runs for a long time and outputs info into the matlab terminal. Most look like this: Location #: Algorithm did not converge. Initial and final likelihoods: ###, ### Running this script, for almost every line, the initial and final

[Freesurfer] mris_preproc xhemi

Dear All, We have been attempting to run a cross hemisphere analysis using .curv files, as per the wiki page: http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi I have outlined the exact steps within our pipeline below. When fitting any glm to the data (simple osgm shown below), we find that

Re: [Freesurfer] mris_preproc xhemi

It could be that there is a problem with one or more of your subjects. First, look at the mask tksurfer fsaverage_sym lh inflated -overlay mask -fminmax .5 1 the mask should extend over almost all cortex except the medial wall. To look at each subject, you can run tksurfer fsaverage_sym lh

[Freesurfer] mris_preproc questions

Pedro Rosa Hi, I have a couple of questions about the mris_preproc: 1) Can I include all subjects in the qdec.table, but afterwards exclude some of them (based on a determined categorial variable) during the statistical analysis? I understood that the script assembles thickness / area data

Re: [Freesurfer] mris_preproc questions

On 01/27/2014 06:03 PM, Pedro Rosa wrote: Pedro Rosa Hi, I have a couple of questions about the mris_preproc: 1) Can I include all subjects in the qdec.table, but afterwards exclude some of them (based on a determined categorial variable) during the statistical analysis? I don't think

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