Re: [Freesurfer] mri_surf2surf error: No such file or directory (but file exists)

Hi Salma, I think mri_surf2surf was complaining /Users/salmasalhi/my_code/HumanBrain_v2/reconall/fsaverage/label/lh.glasser.annot. Can you check if the file exists? The reason for "ERROR: could not determine type of lh.orig" is that mri_info doesn't handle surface file. Best, Yujing From:

Re: [Freesurfer] mri_surf2surf error

22 10:42 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] mri_surf2surf error That mgh file has nothing in it (all dimensions 0). How did you create it? On 5/12/2022 5:20 PM, Zhang, Fan wrote: *External Email - Use Caution * Hi Dr. Greve, I got this when

Re: [Freesurfer] mri_surf2surf error

the “load_mgh” in MATLAB and it showed the dimension is [10242, 1, 1, 78]. Thanks, Fan From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Douglas N. Greve Sent: Thursday, May 12, 2022 10:42 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_surf2surf error That mgh file

Re: [Freesurfer] mri_surf2surf error: could not read surface

It looks like you stopped the job and restarted it. Is that correct? If so, I think something might have gotten out of sync. If you did not make any edits (eg, to correct the defects), then can you start it from scratch? On 5/12/2022 4:29 PM, Margot Wagner wrote: External Email - Use

Re: [Freesurfer] mri_surf2surf error

:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] mri_surf2surf error what happens if you run mri_info lh.CCn_band.Seed1_20220314.V1.13subjs.mgh On 5/3/2022 11:54 AM, Zhang, Fan wrote: External Email - Use Caution Hello Everyone, I am trying to run mri_surf2surf. But I got some

Re: [Freesurfer] mri_surf2surf error

-0. -0. -0. 1. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve Sent: Thursday, May 5, 2022 3:33 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_surf2surf error what happens if you run

Re: [Freesurfer] mri_surf2surf error

what happens if you run mri_info lh.CCn_band.Seed1_20220314.V1.13subjs.mgh On 5/3/2022 11:54 AM, Zhang, Fan wrote: External Email - Use Caution Hello Everyone, I am trying to run mri_surf2surf. But I got some errors saying "no such file or directory" while in fact there are files in

Re: [Freesurfer] mri_surf2surf error - 'could not determine type of...'

That worked like a charm. Thanks! On Wed, Oct 23, 2013 at 5:14 PM, Bruce Fischl wrote: > try specifying --sval-annot Yeo2011_17Networks_N1000.annot instead of > --srcsurfval > > cheers > Bruce > > On Wed, 23 Oct 2013, Paul Beach wrote: > > Apologies: the full error message was: 'could not det

Re: [Freesurfer] mri_surf2surf error - 'could not determine type of...'

try specifying --sval-annot Yeo2011_17Networks_N1000.annot instead of --srcsurfval cheers Bruce On Wed, 23 Oct 2013, Paul Beach wrote: Apologies: the full error message was: 'could not determine type of lh.Yeo2011_17Networks_N1000.annot' I tried your suggestion of removing the hemispheric des

Re: [Freesurfer] mri_surf2surf error - 'could not determine type of...'

Apologies: the full error message was: '*could not determine type of lh.Yeo2011_17Networks_N1000.annot*' I tried your suggestion of removing the hemispheric designation in front of 'Yeo' and I'm getting the same error - - the same occurs if I remove the '.annot' at the end. *mri_surf2surf --srcsu

Re: [Freesurfer] mri_surf2surf error - 'could not determine type of...'

The full error msg is not in the subject line. My guess is that the "lh." in front of "Yeo" in the srcsurfval is causing the problem On 10/23/2013 03:17 PM, Paul Beach wrote: > Hello FS experts, > > I'm attempting to transform the Yeo2011 annotations (lh & rh) from > fsaverage to individual su

Re: [Freesurfer] mri_surf2surf error

Hi Zhu what is your command line? Bruce On Thu, 6 Sep 2012, zzy7...@mail.ustc.edu.cn wrote: > Hi Freesurfers, > > I'm trying to extracting thickness value for a ROI which is created by afni.I > follow the workflows of "Cortical Thickness of a Volume-defined ROI". The ROI > mask and T1 volum

Re: [Freesurfer] mri_surf2surf error

you probably need to redo them since it didn't find the cortex.label it will include the zero thicknesses in the medial wall for example On Fri, 1 Jun 2012, mdkrue...@uwalumni.com wrote: Actually one last question-  I used label2label to transfer some labels and grab ROI thickness averages fro

Re: [Freesurfer] mri_surf2surf error

I see. So you must have overwritten it with something, maybe a stats file. You'll need to rerun mris_make_surfaces or autorecon 3 for that subject/hemi to recreate it. cheers Bruce On Fri, 1 Jun 2012, mdkrue...@uwalumni.com wrote: > Bruce- > > It is, and i agree, for instance here is the lh.co

Re: [Freesurfer] mri_surf2surf error

that makes sense. also just for clarification to a point a made before - i was not using label2label to transfer the rh.cortex.label we have been discussing across subjects, i was transferring other labels, which is most likely why the label2label and measurements didnt fail. I believe i misunderst

Re: [Freesurfer] mri_surf2surf error

not unless you are trying to visualize the label On 06/01/2012 01:16 PM, mdkrue...@uwalumni.com wrote: > Thanks, i am also still able to display the rh in tksurfer without > issue, shouldnt that also fail with the current rh.cortex.label? > > michael > > On Fri, Jun 1, 2012 at 11:57 AM, Douglas N

Re: [Freesurfer] mri_surf2surf error

Thanks, i am also still able to display the rh in tksurfer without issue, shouldnt that also fail with the current rh.cortex.label? michael On Fri, Jun 1, 2012 at 11:57 AM, Douglas N Greve wrote: > I would have expected that to fail. You can check the time stamps to see > if your output is newer

Re: [Freesurfer] mri_surf2surf error

I would have expected that to fail. You can check the time stamps to see if your output is newer or older than rh.cortex.label. If older, it is probably ok. On 06/01/2012 12:53 PM, mdkrue...@uwalumni.com wrote: > Actually one last question- > > I used label2label to transfer some labels and grab

Re: [Freesurfer] mri_surf2surf error

Actually one last question- I used label2label to transfer some labels and grab ROI thickness averages from the labels on the subject with the rh.cortex.label that has been overwritten. I received no errors during this, does this mean that the label transfers and averages are valid, or do i need t

Re: [Freesurfer] mri_surf2surf error

Doug - That does indeed seem to be the problem! Ill just rerun some things here to rectify that. Thanks for all the help everyone! Best- Michael On Fri, Jun 1, 2012 at 11:01 AM, Douglas N Greve wrote: > I think the label file got overwritten at some point. Check the time > stamp and see if it i

Re: [Freesurfer] mri_surf2surf error

I think the label file got overwritten at some point. Check the time stamp and see if it is much different than the other rh files On 06/01/2012 11:55 AM, mdkrue...@uwalumni.com wrote: > Bruce- > > It is, and i agree, for instance here is the lh.cortex.label file > > #label , from subject ?? > 14

Re: [Freesurfer] mri_surf2surf error

Doug- INPUT mri_surf2surf --hemi rh --s UNM_SUPERSAMPLE --sval rh.meth.00.mgh --fwhm 10 --cortex --tval rh.meth.10.mgh OUTPUT srcsubject = UNM_SUPERSAMPLE srcval = rh.meth.00.mgh srctype= trgsubject = UNM_SUPERSAMPLE trgval = rh.meth.10.mgh trgtype= srcsurfreg = sphere.reg trgs

Re: [Freesurfer] mri_surf2surf error

Bruce- It is, and i agree, for instance here is the lh.cortex.label file #label , from subject ?? 149955 22 -10.374 55.016 3.203 0.00 112 -6.294 36.386 -7.809 0.00 114 -6.137 38.556 13.808 0.00 247 -11.304 45.214 -2.709 0.00 248 -6.278 39.973 2.192 0

Re: [Freesurfer] mri_surf2surf error

what is your full command line and terminal output? doug On 06/01/2012 11:49 AM, Bruce Fischl wrote: > that is the rh.cortex.label file? It doesn't look like it > > On Fri, 1 Jun 2012, mdkrue...@uwalumni.com > wrote: > >> Bruce- >> >> Here you go. Subjects recoded. >> >> Graph: name >> >> Dat

Re: [Freesurfer] mri_surf2surf error

that is the rh.cortex.label file? It doesn't look like it On Fri, 1 Jun 2012, mdkrue...@uwalumni.com wrote: > Bruce- > > Here you go. Subjects recoded. > > Graph: name > > Data: path > Variable: Subject > Measurement: external > subject id, class id, variable value, measurement value, stand

Re: [Freesurfer] mri_surf2surf error

Bruce- Here you go. Subjects recoded. Graph: name Data: path Variable: Subject Measurement: external subject id, class id, variable value, measurement value, standard deviation S1 Cl1 0.0 3.10522500831 0.268702566292 S2 Cl1 1.0 2.67585065105 0.396833961125 S3 Cl1 2.0 3.07631433273

Re: [Freesurfer] mri_surf2surf error

Hi Michael can you check to see that your partition is not full? Does the rh.cortex.label file exist in that subject's label dir? If so, what are the first couple of lines? cheers Bruce On Fri, 1 Jun 2012, mdkrue...@uwalumni.com wrote: To anyone who can help - I am trying to tun a GLM on

Re: [Freesurfer] mri_surf2surf error - Return code 254

not and keep the topology (there is some decimation that is used in the EEG/MEG inverse stuff, but it's just to generate points, not faces) On Fri, 9 Dec 2011, Douglas N Greve wrote: > Bruce, do you have a command to reduce the number of vertices? > > John Griffiths wrote: >> >> >> Ok. Can't s

Re: [Freesurfer] mri_surf2surf error - Return code 254

it won't On Fri, 9 Dec 2011, John Griffiths wrote: Ok. Can't see any options in mris_smooth info reducing the number of vertices. How would I do that? Ta,             john On 9 December 2011 17:22, Douglas N Greve wrote: Yes, give it both --sval-xyz and --tval-xyz to indicate that t

Re: [Freesurfer] mri_surf2surf error - Return code 254

Bruce, do you have a command to reduce the number of vertices? John Griffiths wrote: > > > Ok. Can't see any options in mris_smooth info reducing the number of > vertices. How would I do that? > > Ta, >john > > > On 9 December 2011 17:22, Douglas N Greve

Re: [Freesurfer] mri_surf2surf error - Return code 254

Ok. Can't see any options in mris_smooth info reducing the number of vertices. How would I do that? Ta, john On 9 December 2011 17:22, Douglas N Greve wrote: > Yes, give it both --sval-xyz and --tval-xyz to indicate that the output is > a surface. We usually use mris_smooth to smoot

Re: [Freesurfer] mri_surf2surf error - Return code 254

Yes, give it both --sval-xyz and --tval-xyz to indicate that the output is a surface. We usually use mris_smooth to smooth surfaces; I'm not sure whether this use of mri_surf2surf will work properly. doug Bruce Fischl wrote: > Hi John > > Doug can say for sure, but I think you want to give it th

Re: [Freesurfer] mri_surf2surf error - Return code 254

Hi John Doug can say for sure, but I think you want to give it the switch --sval-xyz so it knows to expect a surface not a scalar field over the surface. cheers Bruce On Wed, 7 Dec 2011, John Griffiths wrote: [ Douglas and Dan - sending this again as I didn't sent it to the list address bef

Re: [Freesurfer] mri_surf2surf error - Return code 254

[ Douglas and Dan - sending this again as I didn't sent it to the list address before. Sorry. ] Thanks guys. When I run mri_info on the .mgz file I was using before it seems crash (nothing happens, and have to press ctrl+c to get the console back). So I suppose that partially explains mri_surf2s

Re: [Freesurfer] mri_surf2surf error - Return code 254

surf2surf actually takes surface overlays (not surfaces themselves) as input, and they can be in any format that FS reads. The wiki is probably not up-to-date as those options are ok. doug Daniel Wakeman wrote: > Hi John, > > It seems weird that you are using .mgz files (this suffix is for > vo

Re: [Freesurfer] mri_surf2surf error - Return code 254

What is lh.pial_converted.mgz? How big is it? what do get if you run mri_info on it? doug John Griffiths wrote: > Dear list, > > I am having the following memory allocation problem when running > mri_surf2surf. Can't find any mention of this error on the list or the > internet - sorry if I've

Re: [Freesurfer] mri_surf2surf error - Return code 254

Hi John, It seems weird that you are using .mgz files (this suffix is for volume files) with mri_surf2surf (whose inputs should be surfaces). Also, it seems that several of the options you are trying I don't believe exist at least according to the wiki (e.g. -cortex -fwhm). Are you sure you are us

Re: [Freesurfer] mri_surf2surf - Error

did you create a subject called "average"? This is done with make_average_subject. Alternatively, we distribute an average subject called fsaverage, so you can just use that instead if you want. doug Alexandru Hanganu wrote: Dear Freesurfer Users, We have a little problem with mri_surf2surf.