Re: [Freesurfer] mri_label2vol fillribbon issue

Hi Letitia, Can you send the full command lines that you ran and the output? Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Schneider, Letitia Maria Sent: Thursday, March 14, 2024 10:43 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] mri_label2vol

[Freesurfer] mri_label2vol fillribbon issue

External Email - Use Caution Hello, I am using Freesurfer version 7.3.2 on a mac. I am using the mri_label2vol function to project an anatomical label into volume space, but I realised the label comes out wrong when I use the --fill-ribbon flag: its orientation changes to RSP. T

Re: [Freesurfer] mri_label2vol error

External Email - Use Caution Hi Doug, That solved the problem like a charm. By the way, the volume came from brain.mgz. Thank you! Regards, Sean On Sat, Jan 14, 2023 at 12:28 AM Douglas N. Greve wrote: > What volume did the TF.label come from? Whatever it is, try adding > --tk

Re: [Freesurfer] mri_label2vol error

What volume did the TF.label come from? Whatever it is, try adding --tkr-template volume.nii.gz On 1/12/2023 9:12 PM, Shao-Min (Sean) Hung wrote: External Email - Use Caution Sure. Here's the command line:  -- mri_label2vol --label /Users/xxx/Documents/MRI/UNSTP/data/$subj/bold/Ret

Re: [Freesurfer] mri_label2vol error

External Email - Use Caution Sure. Here's the command line: -- mri_label2vol --label /Users/xxx/Documents/MRI/UNSTP/data/$subj/bold/Retinolabels/TF.label --temp /Users/xxx/Documents/MRI/UNSTP/data/$subj/bold/004/fmc.nii.gz --reg /Users/xxx/Documents/MRI/UNSTP/data/$subj/bold/reg

Re: [Freesurfer] mri_label2vol error

Can you send your command line and full terminal output? On 1/8/2023 9:37 PM, Shao-Min (Sean) Hung wrote: External Email - Use Caution Dear Doug, I have been having the following issue and haven't figured out a way to get around it. I have also searched the archive and did not find

[Freesurfer] mri_label2vol error

External Email - Use Caution Dear Doug, I have been having the following issue and haven't figured out a way to get around it. I have also searched the archive and did not find anything relevant enough to be helpful. The context is, I am drawing functional ROIs on volumetric data

Re: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

. Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Benjamin Deck Sent: Tuesday, June 21, 2022 5:04 PM To: Freesurfer support list Subject: Re: [Freesurfer] mri_label2vol fill-ribbon segmentation fault External Email - Use Caution Hi Yujing, It seems that this did not solve

Re: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

mris_label2annot, ‘—offset 1’ should also >> be specified. >> >> >> >> Yujing >> >> >> >> *From:* Huang, Yujing >> *Sent:* Thursday, June 16, 2022 1:59 PM >> *To:* Freesurfer support list >> *Subject:* RE: [Freesurfer] mri_label2vol

Re: [Freesurfer] mri_label2vol misaligned for subcortical atlas

How was H-O_subcortical_parcellation_thr50.nii  created? Those instructions are for when you have a segmentation in the FS conformed space and you want to get them back to the native space. So your segmentation must be in FS conformed space of the individual On 6/10/2022 6:49 PM, Christopher P

Re: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

ons. > > > > If ‘--no-unknown’ is used with mris_label2annot, ‘—offset 1’ should also > be specified. > > > > Yujing > > > > *From:* Huang, Yujing > *Sent:* Thursday, June 16, 2022 1:59 PM > *To:* Freesurfer support list > *Subject:* RE: [Freesurfer]

Re: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

support list mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] mri_label2vol fill-ribbon segmentation fault External Email - Use Caution Hi Yujing, Thanks for taking a look. What do you mean by mismatch? The LUT was used to make the annot file. What would generate this mism

Re: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

by one. Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Benjamin Deck Sent: Thursday, June 16, 2022 10:58 AM To: Freesurfer support list Subject: Re: [Freesurfer] mri_label2vol fill-ribbon segmentation fault External Email - Use Caution Hi Yujing, Thanks for taking

Re: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

sure what > the right action is to work around this. > > > > Yujing > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Benjamin Deck > *Sent:* Friday, June 10, 2022 11:47 AM > *To:* Fr

Re: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

. Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Benjamin Deck Sent: Friday, June 10, 2022 11:47 AM To: Freesurfer support list Subject: [Freesurfer] mri_label2vol fill-ribbon segmentation fault External Email - Use Caution Hi there, Having issues with the following

Re: [Freesurfer] mri_label2vol with fill-ribbon option

Hi Junjie, Can you specify the Freesurfer version you are running? Thanks. Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Wu, Junjie Sent: Saturday, June 11, 2022 11:15 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] mri_label2vol with fill-ribbon option

[Freesurfer] mri_label2vol with fill-ribbon option

External Email - Use Caution Dear Freesurfer experts,, I tried to use mri_label2vol with fill-ribbon option to covert the surface-based label of perirhinal cortex into the volume (an ROI in mgz file). However, when I typed "mri_label2vol --fill-ribbon --label lh.entorhinal_exvivo.

[Freesurfer] mri_label2vol misaligned for subcortical atlas

External Email - Use Caution Hi Freesurfer Devs, I’m attempting to transform the Harvard-Oxford subcortical atlas (obtained from https://secure-web.cisco.com/1Tup0RI4qms0go1SEsu5ke-k7Cz5iL5tezC3TmgzZcvjKql7cMAvufmLPE-9uQMG30h-oUMoJjztafGtqYW4peNQ-P6hieMkBpEft65mQvR2F9kIM0hcFXxLHR

Re: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

External Email - Use Caution Hi, I would like to unsubscribe from these emails. Thank you. Manuela On Fri, Jun 10, 2022 at 8:47 AM Benjamin Deck wrote: > External Email - Use Caution > > Hi there, > > Having issues with the following command: > > mri_label2vol --annot

[Freesurfer] mri_label2vol fill-ribbon segmentation fault

External Email - Use Caution Hi there, Having issues with the following command: mri_label2vol --annot lh.yeo_2011.annot --temp /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/orig.mgz --hemi lh --fill-ribbon --identity --subject sub-DAEK --o lh.sub-DAEK_annot_nat.nii.gz pro

Re: [Freesurfer] mri_label2vol error

: [Freesurfer] mri_label2vol error External Email - Use Caution Hi, I get the following error message when I run mri_label2vol (freesurfer v 6.0) in a jupyter notebook(6.1.4) with python (v3.8.5): dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from

[Freesurfer] mri_label2vol error

External Email - Use Caution Hi, I get the following error message when I run mri_label2vol (freesurfer v 6.0) in a jupyter notebook(6.1.4) with python (v3.8.5): dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfe

Re: [Freesurfer] mri_label2vol - Questions about label file and missing voxels?

: Re: [Freesurfer] mri_label2vol - Questions about label file and missing voxels? On 3/23/2021 4:54 PM, Devavrat Vartak wrote: External Email - Use Caution Hello freesurfer experts, I am using mri_label2vol to convert my surface drawn label (of functional activity) to

Re: [Freesurfer] mri_label2vol - Questions about label file and missing voxels?

On 3/23/2021 4:54 PM, Devavrat Vartak wrote: External Email - Use Caution Hello freesurfer experts, I am using mri_label2vol to convert my surface drawn label (of functional activity) to functional space (nifti) for more analysis (prf). When I open the label file in text editor -

[Freesurfer] mri_label2vol - Questions about label file and missing voxels?

External Email - Use Caution Hello freesurfer experts, I am using mri_label2vol to convert my surface drawn label (of functional activity) to functional space (nifti) for more analysis (prf). When I open the label file in text editor - it shows two lines at the top #!ascii label

Re: [Freesurfer] mri_label2vol

It looks like it should work. The only other thing I would suggest is to use --regheader orig.mgz instead of --identity (though I would have thought --identity would have worked). On 4/29/2020 2:12 PM, Mason Wells wrote: External Email - Use Caution Hi Experts, I want to take an ROI

[Freesurfer] mri_label2vol

External Email - Use Caution Hi Experts, I want to take an ROI label that I have drawn on the surface and transform this into the volume. I have drawn the label in the T1 anatomical space and I want to keep the label in this space during the conversion. I am currently using thi

Re: [Freesurfer] mri_label2vol error: could not scan # of lines from label file

Hi Joshua hmmm, label2vol takes our text label file format as input, not a .gii file. You probably need to ask the Wash U HCP folks how to do this conversion as I believe there should be a step before label2vol cheers Bruce On Thu, 9 Mar 2017, Burks, Joshua D (HSC) wrote: Hello FreeSurf

[Freesurfer] mri_label2vol error: could not scan # of lines from label file

Hello FreeSurfer Developers, I’m attempting to convert a dlabel file from the Human Connectome Project to a volumetric ROI that I can use for fiber tractography on other platforms. I followed the tutorial provided by HCP (hcp-users FAQ #9: How do I map data between FreeSurfer ... - HCP Wiki

Re: [Freesurfer] mri_label2vol check-up

Dear. Experts. Please ignore the previous email. It works. Thank you. Best, Ji Won 2016-03-23 17:24 GMT-04:00 Ji Won Bang : > Dear. Freesurfer experts. > > Hi. How are you? > > I'd appreciate it a lot if you can help me with this problem. > > I'm trying to check the ROI (.nii) after creating

[Freesurfer] mri_label2vol check-up

Dear. Freesurfer experts. Hi. How are you? I'd appreciate it a lot if you can help me with this problem. I'm trying to check the ROI (.nii) after creating it by using mri_label2vol command. I used the command: mri_label2vol --label $SUBJECTS_DIR/$SUBJECT/label/lh.v1vt.label --label $SUBJECTS_D

Re: [Freesurfer] mri_label2vol projfrac missing voxels

Hi, I just wanted to post back the problem was solved (Thanks Doug). The solution is this: 1. use mri_aparc2aseg mri_aparc2aseg --s $SUBJECT --o .mgz --annot --annot-table [Note, in my case I was using 3 different values, 1, 2, 3 for the labels with only left hemisphere labels (the details wi

[Freesurfer] mri_label2vol projfrac missing voxels

Hi, I am having trouble with the projfrac option in mri_label2vol (on the current dev freesurfer environment). When I use the following command: mri_label2vol --annot label/lh.lang.annot --subject nmr00937 --o lang_seg.mgz --hemi lh --identity --temp mri/T1.mgz --proj frac 0 1 .01 I get many mis

Re: [Freesurfer] mri_label2vol --fill-ribbon argument

if this refers to a previous email, then make sure to include previous correspondence. in any event, I don't know what you did and can't help you until I find out On 12/14/2015 06:11 PM, Arnaud Boré wrote: > Dear Freesurfer's experts, > > I wanted to add this picture so you can understand better

[Freesurfer] mri_label2vol --fill-ribbon argument

Dear Freesurfer's expert, I want to create a 3d volume using an annot file and I'm using mri_label2vol command. When running this command line: mri_label2vol --annot sub1/label/lh.Yeo2011_7Networks_N1000.annot --identity --subject sub1 --hemi lh --o sub1/mri/lh.Yeo.nii.gz --temp sub1/mri/T1.mgz

[Freesurfer] mri_label2vol change to MNI 152

Hi Freesurfer listserve, I hope you are well. I emailed the freesurfer listserve also but got no response. I am trying to take an functional ROI that is anatomically constrined that I created using tkmedit and transform it to MNI152 space. I saved it as $label.label. Then did this command: m

[Freesurfer] mri_label2vol in matlab

Hi Freesurfer experts, I have a label with 1500+ vertices I'd like to convert to a nifti file. Right now I use mri_label2vol and output a file I'd like to do this in matlab, is there any way? More specifically, I'd like to get the native co-ordinate for each vertex in the nifti file. The vox2ras co

[Freesurfer] mri_label2vol unable to read in all labels

Hi, I am trying to combine 236 labels into one volume (for the left hemisphere). However after 233 volumes I get an 'Segmentation fault (core dumped)' which I believe is related to a memory issue. If it is relevant I am using a GIFTI image as the surface (I am using HCP data). mri_label2vol $(cat

[Freesurfer] mri_label2vol - output volume appears cut off

Hi all, I am having a problem with moving aparc+aseg to different dimensions. I have successfully resliced aparc+asegs for several other subjects, but the resliced volume for one subject appears cut-off at the bottom. The dimensions match for this subject's template and output volumes, and the o

[Freesurfer] mri_label2vol not working

Hi Doug, I have tried the command that you suggested below. Still not working. System gave the same error message again "segment fault". Any other ideas? Best wishes, Jingjing * try running this command mri_label2vol --label lh.words10_10.label --temp rawavg.mgz --reg rawreg.dat --fillthresh .5

Re: [Freesurfer] mri_label2vol problem

De : Douglas N Greve À : LAOUCHEDI MAKHLOUF Cc : "freesurfer@nmr.mgh.harvard.edu" Envoyé le : Vendredi 28 juin 2013 21h23 Objet : Re: [Freesurfer] mri_label2vol problem Hi Laouchedi, I still cannot figure out why you are getting a volume of all 0s. Are you sure it is all 0s an

Re: [Freesurfer] mri_label2vol problem

013 18h41 Objet : Re: [Freesurfer] mri_label2vol problem Hi Laouchedi, I have asked you two times now to include all previous correspondences in each email. This is the 3rd time. If you are going to make it hard for us to answer your question, then the result will be that they won't be answ

Re: [Freesurfer] mri_label2vol problem

ve À : freesurfer@nmr.mgh.harvard.edu Envoyé le : Vendredi 28 juin 2013 16h49 Objet : Re: [Freesurfer] mri_label2vol problem How does the annot look on the surface (ie, intksurfer)? What is the full terminal output of mri_label2vol? On 06/28/2013 10:19 AM, LAOUCHEDI MAKHLOUF wrote: > Hi >

[Freesurfer] mri_label2vol problem

excuse me but i don't understand what you mean by "terminal of mri_label2vol" Thank you for help ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is i

Re: [Freesurfer] mri_label2vol problem

How does the annot look on the surface (ie, intksurfer)? What is the full terminal output of mri_label2vol? On 06/28/2013 10:19 AM, LAOUCHEDI MAKHLOUF wrote: > Hi > i run mri_label2annot to get individual annot files for all > labels, then i run mri_label2vol to get nifti volumes of my labe

[Freesurfer] mri_label2vol problem

Hi i run mri_label2annot to get individual annot files for all labels, then i run mri_label2vol to get nifti volumes of my labels using the following command :   mri_label2vol --annot  lh.G_and_S_cingul-Ant.annot --temp SUBJ_DIR/ctr2/mri/brain.mgz --subject ctr2 --hemi lh --identity --

Re: [Freesurfer] mri_label2vol: Brodmann Areas

You will have to merge the labels into an annotation (mris_label2annot), then the annotation to a segmentation volume (mri_aparc2aseg), then apply mri_label2vol to the segmentation. doug On 02/19/2013 10:45 AM, Vincent Koppelmans wrote: > Hi all, > > I am trying to convert Brodmann area 4a and

[Freesurfer] mri_label2vol: Brodmann Areas

Hi all, I am trying to convert Brodmann area 4a and 4p to .nii file format in native space. I have used to following syntax: tkregister2 --mov ${SUBJECTS_DIR}/mri/rawavg.mgz --noedit --s [SUBJECT_ID] --regheader --reg ./register.dat mri_label2vol --label [PATH-TO-LABEL-FILE] --temp ${SUBJECT

Re: [Freesurfer] mri_label2vol

thanks it works now :) On 04/12/2012 12:48 PM, Douglas N Greve wrote: > Take the inverse > > On 04/12/2012 01:47 PM, Johnson wrote: >> I do the transformation in Matlab, I found out that the matlab >> *load_mgh* function returns the vox2ras matrix, where can I find the >> ras2vox matrix? >> >> On 0

Re: [Freesurfer] mri_label2vol

Take the inverse On 04/12/2012 01:47 PM, Johnson wrote: > I do the transformation in Matlab, I found out that the matlab > *load_mgh* function returns the vox2ras matrix, where can I find the > ras2vox matrix? > > On 04/12/2012 12:11 PM, Bruce Fischl wrote: >> yes >> On Thu, 12 Apr 2012, Johnson

Re: [Freesurfer] mri_label2vol

I do the transformation in Matlab, I found out that the matlab *load_mgh* function returns the vox2ras matrix, where can I find the ras2vox matrix? On 04/12/2012 12:11 PM, Bruce Fischl wrote: yes On Thu, 12 Apr 2012, Johnson wrote: The vector coordinates will be in the voxel space On 04/12/

Re: [Freesurfer] mri_label2vol

yes On Thu, 12 Apr 2012, Johnson wrote: > The vector coordinates will be in the voxel space > > On 04/12/2012 11:54 AM, Bruce Fischl wrote: >> Hi Johnson >> >> it depends whether you are using the ras2vox or vox2ras. It should be: >> >> V_rawavg = M_ras2vox_rawavg * inv(M_ras2vox_aseg) * V_aseg

Re: [Freesurfer] mri_label2vol

The vector coordinates will be in the voxel space On 04/12/2012 11:54 AM, Bruce Fischl wrote: > Hi Johnson > > it depends whether you are using the ras2vox or vox2ras. It should be: > > V_rawavg = M_ras2vox_rawavg * inv(M_ras2vox_aseg) * V_aseg > > Where the V_* are 4x1 homogenous vectors. > > ch

Re: [Freesurfer] mri_label2vol

Hi Johnson it depends whether you are using the ras2vox or vox2ras. It should be: V_rawavg = M_ras2vox_rawavg * inv(M_ras2vox_aseg) * V_aseg Where the V_* are 4x1 homogenous vectors. cheers Bruce On Thu, 12 Apr 2012, Johnson wrote: > so to be clear about it, suppose T1 is the matrix in aseg

Re: [Freesurfer] mri_label2vol

so to be clear about it, suppose T1 is the matrix in aseg and T2 is the one in rawavg, to transform from aseg to rawavg I will apply invert(T1)*T2 is that correct? On 4/11/2012 8:12 PM, Bruce Fischl wrote: >> Invert one and compose it with the other >> >> >> >> On Apr 11, 2012, at 7:48 PM, John

Re: [Freesurfer] mri_label2vol

so to be clear about it, suppose T1 is the matrix in aseg and T2 is the one in rawavg, to transform from aseg to rawavg I will apply invert(T1)*T2 is that correct? On 4/11/2012 8:12 PM, Bruce Fischl wrote: > Invert one and compose it with the other > > > > On Apr 11, 2012, at 7:48 PM, Johnson wr

Re: [Freesurfer] mri_label2vol

Invert one and compose it with the other On Apr 11, 2012, at 7:48 PM, Johnson wrote: > there are two transformation matrices one in aseg and one in rawavg, how do I > use them ? > > On 04/11/2012 6:12 PM, Bruce Fischl wrote: >> yes >> On Wed, 11 Apr 2012, Johnson wrote: >> >>> great, so if

Re: [Freesurfer] mri_label2vol

there are two transformation matrices one in aseg and one in rawavg, how do I use them ? On 04/11/2012 6:12 PM, Bruce Fischl wrote: > yes > On Wed, 11 Apr 2012, Johnson wrote: > >> great, so if I can read the header from the aseg file and the header from the >> rawavg header file I would be able

Re: [Freesurfer] mri_label2vol

yes On Wed, 11 Apr 2012, Johnson wrote: > great, so if I can read the header from the aseg file and the header from the > rawavg header file I would be able to transfer any point from the aseg space > to the rawavg space is that correct ? > > On 04/11/2012 4:40 PM, Bruce Fischl wrote: >> it regi

Re: [Freesurfer] mri_label2vol

Yes, that is correct. On 04/11/2012 06:54 PM, Johnson wrote: > great, so if I can read the header from the aseg file and the header > from the rawavg header file I would be able to transfer any point from > the aseg space to the rawavg space is that correct ? > > On 04/11/2012 4:40 PM, Bruce Fisch

Re: [Freesurfer] mri_label2vol

great, so if I can read the header from the aseg file and the header from the rawavg header file I would be able to transfer any point from the aseg space to the rawavg space is that correct ? On 04/11/2012 4:40 PM, Bruce Fischl wrote: > it registers them based on the header information, but sin

Re: [Freesurfer] mri_label2vol

it registers them based on the header information, but since the aseg is derived from the rawavg that should be exactly correct On Wed, 11 Apr 2012, Johnson wrote: > And it exactly does that, does it register them together or use a pre-known > transformation matrix > On 04/11/2012 3:46 PM, Bru

Re: [Freesurfer] mri_label2vol

And it exactly does that, does it register them together or use a pre-known transformation matrix On 04/11/2012 3:46 PM, Bruce Fischl wrote: > Hi Johnson > > I believe it resamples the aseg to have the same geometry as the > original scan. > > cheers > Bruce > On Wed, 11 Apr 2012, Johnson wrote:

Re: [Freesurfer] mri_label2vol

Hi Johnson I believe it resamples the aseg to have the same geometry as the original scan. cheers Bruce On Wed, 11 Apr 2012, Johnson wrote: Hi Can someone tell me please in details what does this line do?  mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o aseg-in-rawavg.mgz --reg header

[Freesurfer] mri_label2vol

Hi Can someone tell me please in*_details_*what does this line do? mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o aseg-in-rawavg.mgz --regheader aseg.mgz thanks -- Johnson J. GadElkarim Research Assistant, Department Of Psychiatry, PhD Candidate, Department Of Electrical& Computer Eng., U

Re: [Freesurfer] mri_label2vol cannot allocate memory

if you email me the .mgz I'll fix it. On Fri, 6 Apr 2012, Anthony Dick wrote: > Hello--was wondering if you guys have any ideas. I am a bit stumped. > Thanks for the help! > > Anthony > > On 4/4/12 4:50 PM, Anthony Dick wrote: >> No, but the conversion from the original .nii works... >> >> [mile

Re: [Freesurfer] mri_label2vol cannot allocate memory

can you upload chuman_1.nii to our file drop? On 04/06/2012 11:30 AM, Anthony Dick wrote: > Hello--was wondering if you guys have any ideas. I am a bit stumped. > Thanks for the help! > > Anthony > > On 4/4/12 4:50 PM, Anthony Dick wrote: >> No, but the conversion from the original .nii works...

Re: [Freesurfer] mri_label2vol cannot allocate memory

Hello--was wondering if you guys have any ideas. I am a bit stumped. Thanks for the help! Anthony On 4/4/12 4:50 PM, Anthony Dick wrote: > No, but the conversion from the original .nii works... > > [miles:[PATH]] adick% mri_convert chuman_1.mgz junk.mgh > mri_convert chuman_1.mgz junk.mgh > $Id:

Re: [Freesurfer] mri_label2vol cannot allocate memory

What version are you using? One of our versions had a problem with creating bad mgzs. You probably don't need to convert it to mgz. Can you run mri_label2vol with the original nii and see if it works? doug On 04/04/2012 04:50 PM, Anthony Dick wrote: > No, but the conversion from the original .ni

Re: [Freesurfer] mri_label2vol cannot allocate memory

No, but the conversion from the original .nii works... [miles:[PATH]] adick% mri_convert chuman_1.mgz junk.mgh mri_convert chuman_1.mgz junk.mgh $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from chuman_1.mgz... MRIallocIndices: could not allocate 1701979223 elt index arra

Re: [Freesurfer] mri_label2vol enquiry

so how it is used here? mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o aseg-in-rawavg.mgz --regheader aseg.mgz On 04/04/2012 3:38 PM, Douglas N Greve wrote: > If you pass it a registration (--reg) then it uses that. It can also > compute a registration from the information about the geometr

Re: [Freesurfer] mri_label2vol cannot allocate memory

Can you successfully run mri_convert on chuman_1.mgz, eg mri_convert chuman_1.mgz junk.mgh doug On 04/04/2012 12:29 PM, Anthony Dick wrote: > Hello Bruce, > > Sorry--just getting back to this project. The basic problem is that I am > trying to align a cerebellar parcellation with the underlay i

Re: [Freesurfer] mri_label2vol enquiry

If you pass it a registration (--reg) then it uses that. It can also compute a registration from the information about the geometry in the header (--regheader) (assuming that the two volumes share a coordinate system). doug On 04/04/2012 01:48 PM, Johnson wrote: > Hi > Can anyone tell me please

[Freesurfer] mri_label2vol enquiry

Hi Can anyone tell me please how mri_label2vol works, I know what it does, but I need to know how it works to take the FS space to the original anatomy space: does it do registration or does it use a transformation matrix. If the latest which one, where can I find it? regards -- Johnson J. Ga

Re: [Freesurfer] mri_label2vol cannot allocate memory

Hello Bruce, Sorry--just getting back to this project. The basic problem is that I am trying to align a cerebellar parcellation with the underlay in tkmedit. I was working on this with Doug, and his suggestion actually worked, and now I can't get it to work again (see thread: http://www.mail-a

Re: [Freesurfer] mri_label2vol cannot allocate memory

Hi Anthony, what's in chuman_1.mgz? How many labels? doug Anthony Dick wrote: > Hello--I am giving this message a bump. Please let me know if there are > any suggestions. Thanks! > > Anthony > > On 2/15/12 1:43 PM, Anthony Dick wrote: > >> Hello, >> >> I have run the following successfully, bu

Re: [Freesurfer] mri_label2vol cannot allocate memory

Hi Anthony sounds like there is something wrong with one of your volumes. Can you ru mri_info on them? Bruce On Wed, 7 Mar 2012, Anthony Dick wrote: > Hello--I am giving this message a bump. Please let me know if there are > any suggestions. Thanks! > > Anthony > > On 2/15/12 1:43 PM, Anthony D

Re: [Freesurfer] mri_label2vol cannot allocate memory

Hello--I am giving this message a bump. Please let me know if there are any suggestions. Thanks! Anthony On 2/15/12 1:43 PM, Anthony Dick wrote: > Hello, > > I have run the following successfully, but when I have moved on to other > brains I get: > > mri_label2vol --seg chuman_1.mgz --temp orig.

[Freesurfer] mri_label2vol cannot allocate memory

Hello, I have run the following successfully, but when I have moved on to other brains I get: mri_label2vol --seg chuman_1.mgz --temp orig.mgz --regheader > chuman_1.mgz --o chuman_1.conf.mgz MRIalloc: could not allocate 975187978 frame Cannot allocate memory I am running a Mac Pro with 8GB R

Re: [Freesurfer] mri_label2vol: how to make the opposite direction?

Thank you. I succeeded to convert it, but the label is completely incorrect. Actually, I can not understand how exactly it can work: when I make an opposite direction with mri_label2vol I pass the registrer.dat file; however, in mri_cor2label there is no such option. How then this transformation ca

Re: [Freesurfer] mri_label2vol: how to make the opposite direction?

The id is the value in the mask. So if it's a binary mask, use --id 1 John Gelburg wrote: > I am sorry, but I still struggle to make it work :( > Here is my syntax: > mri_cor2label --i my_Analyze_mask.nii --l ./freeSurferMask.label > I am getting "ERROR: must supply a label id" error message. >

Re: [Freesurfer] mri_label2vol: how to make the opposite direction?

what is the value of the binary volume? You have to tell mri_cor2label that with --id I think. cheers Bruce On Sun, 11 Apr 2010, John Gelburg wrote: > I am sorry, but I still struggle to make it work :( > Here is my syntax: > mri_cor2label --i my_Analyze_mask.nii --l ./freeSurferMask.label > I

Re: [Freesurfer] mri_label2vol: how to make the opposite direction?

I am sorry, but I still struggle to make it work :( Here is my syntax: mri_cor2label --i my_Analyze_mask.nii --l ./freeSurferMask.label I am getting "ERROR: must supply a label id" error message. I do not have any label id, because it's my custom mask, which was created in the SPM. On Fri, Apr 9,

Re: [Freesurfer] mri_label2vol: how to make the opposite direction?

It will still work. from mri_cor2label --help : Note: the name of this program is a bit misleading as it will operate on anything readble by mri_convert (eg, mgz, mgh, nifti, bhdr, analyze, etc). John Gelburg wrote: > thanks, but isn't COR volume and my ANALYZE image is not the same thing? > >

Re: [Freesurfer] mri_label2vol: how to make the opposite direction?

thanks, but isn't COR volume and my ANALYZE image is not the same thing? On Fri, Apr 9, 2010 at 8:02 PM, Douglas N Greve wrote: > try mri_cor2label > > John Gelburg wrote: > >> Hi, >> >> I have ANLYZE binary mask which I would like to convert to FreeSurfer >> labels. Is there any more automatic w

Re: [Freesurfer] mri_label2vol: how to make the opposite direction?

try mri_cor2label John Gelburg wrote: > Hi, > > I have ANLYZE binary mask which I would like to convert to FreeSurfer > labels. Is there any more automatic way to do it than loading it as an > overlay and then selecting manually as a label? > > Thanks for help, > John > -

[Freesurfer] mri_label2vol: how to make the opposite direction?

Hi, I have ANLYZE binary mask which I would like to convert to FreeSurfer labels. Is there any more automatic way to do it than loading it as an overlay and then selecting manually as a label? Thanks for help, John ___ Freesurfer mailing list Freesurfer

Re: [Freesurfer] Mri_label2vol memory error

ard.edu im Auftrag von Alex Fornito > Gesendet: Do 22.10.2009 14:34 > An: Douglas N Greve > Cc: freesurfer@nmr.mgh.harvard.edu > Betreff: Re: [Freesurfer] Mri_label2vol memory error > > > > Hi again, > I have noticed that the standard freesurfer annots have the same number of

Re: [Freesurfer] Mri_label2vol memory error

@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] Mri_label2vol memory error Hi again, I have noticed that the standard freesurfer annots have the same number of regions in each hemi. In my annot, I have different numbers; e.,g 1171 in the left and 1187 in the right. Is this what's causing the outp

Re: [Freesurfer] Mri_label2vol memory error

Hi again, I have noticed that the standard freesurfer annots have the same number of regions in each hemi. In my annot, I have different numbers; e.,g 1171 in the left and 1187 in the right. Is this what's causing the output of mri_aparc2aseg to label all right hemi cortical voxels with a 2000 (out

Re: [Freesurfer] Mri_label2vol memory error

Hi again, After running the command, the output image seems to have the left hemi cortex parcellated, but the right is all assigned one intensity (2000). Is there something I'm missing? Output below. Thanks again, Alex mri_aparc2aseg --s fsaverage --rip-unknown --annot 1000_compact.aparc --volmas

Re: [Freesurfer] Mri_label2vol memory error

I just created a ribbon.mgz (link below). Copy this into fsaverage/mri and see if it works. doug ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ribbon.mgz Alex Fornito wrote: > Thanks, that did the trick. > The only problem is that I would also like to do the same for fsaverage,

Re: [Freesurfer] Mri_label2vol memory error

Thanks, that did the trick. The only problem is that I would also like to do the same for fsaverage, but in this case mri_aparc2aseg fails because it is looking for ribbon.mgz (see below). Is there a work around for this? Thanks again, Alex mri_aparc2aseg --s fsaverage/ --rip-unknown --annot 1000

Re: [Freesurfer] Mri_label2vol memory error

Alex, Can you send me the orig.mgz and .annot file used as input to this? To the file drop: https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Nick On Mon, 2009-10-19 at 13:38 +0100, Alex Fornito wrote: > Hi all, > I've tried running mri_label2vol on a few different computers now an

Re: [Freesurfer] Mri_label2vol memory error

how many labels are in that annot? The way that mri_label2vol works is to create a multi-frame volume with the number of frames equal to the number of labels in the annotation. It then counts the number of times each voxel "sees" a given label. It then assigns that voxel to the most frequently

[Freesurfer] Mri_label2vol memory error

Hi all, I've tried running mri_label2vol on a few different computers now and keep encountering the same memory error. Can anyone provide suggestions as to how to get around this problem? I've included the output from a run using linux on a dual 3.05 GHz Xeon with 8GB ram below. Thanks for your hel

Re: Fwd: [Freesurfer] mri_label2vol

Hi Natalia, does the label line up in the volume when viewed with tkmedit? How are you mapping it into standard coords? Are you using mri_label2label? cheers, Bruce On Wed, 8 Jul 2009, Natalia Sanchez wrote: Hi FreeSurfer experts! I am kind of new to FreeSurfer and this is my first time us

Re: [Freesurfer] mri_label2vol

Have you looked at the --help? There's quite a bit of documentation there. Take a look and write back if you still have questions. doug Natalia Sanchez wrote: Hi: I am using mri_label2vol to create cortical regions of interest of M1. What should I use for the template? (--temp argument?) Th

Re: [Freesurfer] mri_label2vol

any of the conformed volumes should be fine, since they all have the same geometry (orig.mgz, brain.mgz, ...) On Wed, 8 Jul 2009, Natalia Sanchez wrote: Hi: I am using mri_label2vol to create cortical regions of interest of M1. What should I use for the template? (--temp argument?) Thank you

[Freesurfer] mri_label2vol

Hi: I am using mri_label2vol to create cortical regions of interest of M1. What should I use for the template? (--temp argument?) Thank you -- Natalia Sanchez ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/m

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