Re: [Freesurfer] mri_cvs_register failure

You can map the curvature from fsaverage to the individual (or reverse) and then load both on the surface to see if they agree. I think that CVS will/can save intermediate registrations, so you might check those to see if the problem is cropping up at a particular step. On 11/9/2023 8:18 AM, A

Re: [Freesurfer] mri_cvs_register failure

I'm not sure what happened. Have you checked the surface-based registration? Also check the talairach reg. On 10/19/2023 11:35 AM, Antonín Škoch wrote: External Email - Use Caution Dear experts, I have encountered an failure of mri_cvs_register --mov my_subject --mni The resulting

Re: [Freesurfer] mri_cvs_register cost function

i Antonio < > fedediantoni...@gmail.com> > *Sent:* Friday, March 24, 2023 5:37 AM > *To:* Freesurfer support list > *Subject:* [Freesurfer] mri_cvs_register cost function > > > External Email - Use Caution > > Dear experts, > > May I ask you which c

Re: [Freesurfer] mri_cvs_register cost function

: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Federica Di Antonio Sent: Friday, March 24, 2023 5:37 AM To: Freesurfer support list Subject: [Freesurfer] mri_cvs_register cost function External Email - Use Caution Dear experts, May I ask you which cost function is used by

[Freesurfer] mri_cvs_register cost function

External Email - Use Caution Dear experts, May I ask you which cost function is used by mri_cvs_register? Thank you so much for your support! Federica Di Antonio ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nm

Re: [Freesurfer] mri_cvs_register with sub-millimeter recons

: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] mri_cvs_register with sub-millimeter recons External Email - Use Caution Hello Freesurfer Experts, I have been trying to run mri_cvs_register to bring sub-millimeter data into MNI space, however the final outputs have large deformations

Re: [Freesurfer] mri_cvs_register for fMRI

Lilla *From:* freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Peter Sperrer *Sent:* Wednesday, August 5, 2020 11:28 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] mri_cvs_register for fMRI External Email - Use Caution Dear Lilla, Thank you for your

Re: [Freesurfer] mri_cvs_register for fMRI

, Lilla *From:* freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Peter Sperrer *Sent:* Wednesday, August 5, 2020 11:28 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] mri_cvs_register for fMRI

Re: [Freesurfer] mri_cvs_register for fMRI

: Wednesday, August 5, 2020 11:28 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_cvs_register for fMRI External Email - Use Caution Dear Lilla, Thank you for your quick response. Now I tried using bbregister --s [SUBJECT] --mov [realignedFunctional.nii] --init

Re: [Freesurfer] mri_cvs_register for fMRI

-structural transform. Best, Lilla *From:* freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Peter Sperrer *Sent:* Wednesday, August 5, 2020 9:17 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer

Re: [Freesurfer] mri_cvs_register for fMRI

@nmr.mgh.harvard.edu *Subject:* [Freesurfer] mri_cvs_register for fMRI External Email - Use Caution Dear FreeSurfer experts, My goal is to morph fMRI (data in voxel space) for best possible intersubject GM-overlap. I am using /mri_cvs_register/ as it seemed like a perfect tool for this. I have

Re: [Freesurfer] mri_cvs_register for fMRI

From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Peter Sperrer Sent: Wednesday, August 5, 2020 9:17 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] mri_cvs_register for fMRI External Email - Use Caution Dear FreeSurfer experts, My

[Freesurfer] mri_cvs_register for fMRI

External Email - Use Caution Dear FreeSurfer experts, My goal is to morph fMRI (data in voxel space) for best possible intersubject GM-overlap. I am using /mri_cvs_register/ as it seemed like a perfect tool for this. I have already run /recon-all /on the anatomical scan (160x2

Re: [Freesurfer] mri_cvs_register: no such file or directory

External Email - Use Caution Hi, I figured out the mistake. I had to remove the forward slashes from the command line. Its running fine now. Thanks, Vinny On Sat, Nov 16, 2019 at 12:13 AM Vinny K wrote: > Hi, > > The moving subjectid directory (subjb) has a cvs folder writt

Re: [Freesurfer] mri_cvs_register: no such file or directory

External Email - Use Caution Hi, The moving subjectid directory (subjb) has a cvs folder written but it is empty. The template subjectid directory has the normal folder structure after recon-all. [image: moving.png] [image: template.png] On Fri, Nov 15, 2019 at 9:54 PM Nader R

Re: [Freesurfer] mri_cvs_register: no such file or directory

External Email - Use Caution Hi Check your subject and template address directory. On Sat, 16 Nov 2019, 01:05 Vinny K External Email - Use Caution > > Hi, > > I'm using the development version of FreeSurfer and am attempting to > register two subjects using mri_cvs_regis

Re: [Freesurfer] mri_cvs_register: no such file or directory

External Email - Use Caution Hi, I'm using the development version of FreeSurfer and am attempting to register two subjects using mri_cvs_register. This is the command I ran: mri_cvs_register --mov subjb/ --template subja/ Below was the outputted message: The outdir: /home/vin

Re: [Freesurfer] [mri_cvs_register] Transform is zero

Hi Stefano, If you suspect that the error is due to the small deformation values, can you try to use -odt float to specify the output data format? Lilla On Tue, 29 Oct 2019, Stefano Zappala wrote: Hi there, I am having problem reading the final_CVSmorph_toS131032017_Supine.m3z transfor

Re: [Freesurfer] mri_cvs_register error while diffusion imaging processing

From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Renew Andrade Sent: Thursday, October 24, 2019 11:31 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] mri_cvs_register error while diffusion imaging processing External Email - Use Caution Dear

[Freesurfer] mri_cvs_register error while diffusion imaging processing

External Email - Use Caution Dear FreeSurfer experts: I am trying to run Spatial Normalization but I cannot get the morph file because I get this error. I don’t know what to do with these libraries. Do I need to copy them from where they are in freesurfer to somewhere else in the

Re: [Freesurfer] mri_cvs_register using fsaverage

of Lilla Zollei Sent: Sunday, August 19, 2018 3:16:31 AM To: Freesurfer support list Subject: Re: [Freesurfer] mri_cvs_register using fsaverage Hi Noam, What version of FS are you using? I have incorporated a change into dev in January. Have you seen this note? https://mail.nmr.mgh.harvar

Re: [Freesurfer] mri_cvs_register using fsaverage

aturday, August 18, 2018 3:08:22 PM To: Freesurfer support list Subject: Re: [Freesurfer] mri_cvs_register using fsaverage   Thanks Lilla! A follow-up question: How can I use the applyMorph function to morph the points to the MNI152 space? I'm trying to use the combined_tocvs_avg35_inMN

Re: [Freesurfer] mri_cvs_register using fsaverage

52.txt against cvs_avg35_inMNI152/mri/brainmask.mgz, at least half of them were outside the brain. Any ideas? Thanks, Noam From: Peled, Noam Sent: Saturday, August 18, 2018 3:08:22 PM To: Freesurfer support list Subject: Re: [Freesurfer] mri_cvs_register using fsa

Re: [Freesurfer] mri_cvs_register using fsaverage

om: freesurfer-boun...@nmr.mgh.harvard.edu > on behalf of Lilla Zollei > > Sent: Wednesday, August 1, 2018 8:35:49 AM > To: Freesurfer support list > Subject: Re: [Freesurfer] mri_cvs_register using fsaverage > > Hi Noam, > > Can you can use the --mni flag? > >

Re: [Freesurfer] mri_cvs_register using fsaverage

AM To: Freesurfer support list Subject: Re: [Freesurfer] mri_cvs_register using fsaverage   Hi Noam, Can you can use the --mni flag? "Use the CVS atlas in MNI152 space as a target for registration (as opposed to the default CVS template)" Lilla On Wed, 1 Aug 2018, Peled, Noam wrote:

Re: [Freesurfer] mri_cvs_register using fsaverage

mgh.harvard.edu on behalf of Douglas N. Greve Sent: Wednesday, August 1, 2018 11:19:16 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_cvs_register using fsaverage FYI, fsaverage is already in MNI305 space On 08/01/2018 11:14 AM, Peled, Noam wrote: > > Thanks Lilla! >

Re: [Freesurfer] mri_cvs_register using fsaverage

t; MNI305 and not MNI152? > > > Thanks again, > > Noam > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu > on behalf of Lilla Zollei > > *Sent:* Wednesday, August 1, 2018 8:35:49 AM >

Re: [Freesurfer] mri_cvs_register using fsaverage

behalf of Lilla Zollei Sent: Wednesday, August 1, 2018 8:35:49 AM To: Freesurfer support list Subject: Re: [Freesurfer] mri_cvs_register using fsaverage Hi Noam, Can you can use the --mni flag? "Use the CVS atlas in MNI152 space as a target for registration (as opposed to the defaul

Re: [Freesurfer] mri_cvs_register using fsaverage

Hi Noam, Can you can use the --mni flag? "Use the CVS atlas in MNI152 space as a target for registration (as opposed to the default CVS template)" Lilla On Wed, 1 Aug 2018, Peled, Noam wrote: I need to transfer one of our patient's electrodes locations (depth electrodes, they aren't loc

[Freesurfer] mri_cvs_register using fsaverage

I need to transfer one of our patient's electrodes locations (depth electrodes, they aren't located on the cortical surface) to MNI305 space. For that, I'm trying to use mri_cvs_register to register the patient to fsaverage. I'm using to the following command: mri_cvs_register --mov subjid --te

[Freesurfer] mri_cvs_register error

Hello, I am trying to run mri_cvs_register on a subject and I got an error (please see attached log file). Below was the command I used. Thank you. mri_cvs_register --mov 01091p --mni --step1 --step2 --step3 --outdir /Users/MiracleOz/Documents/improvervsdeclinermri/01091p/cvs --asegfname aparc+as

[Freesurfer] mri_cvs_register error: Symbol not found: ___emutls_get_address

Hi Freesurfer Developers, I am trying use mri_cvs_register but I ran into an error (Mac OS SIERRA 10.12.2). The log is pasted below. Logfile for mri_cvs_register Sat 10 Jun 2017 17:58:48 BST --mov 16084 $Id: mri_cvs_register,v 1.48 2016/03/06 21:31:56 lzollei Exp $ dhcp-10-240-198-151.cp.wireles

Re: [Freesurfer] mri_cvs_register failure from missing shared lib

The comman was mri_cvs_register --mov MAE_06072013 --mni (because labels in MNI space were mapping incorrectly to subject space -- see this thread https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg52786.html ) The log is attached. I killed the command once I saw the errors. Thanks!

Re: [Freesurfer] mri_cvs_register failure from missing shared lib

Hi Corinna, Its been awhile since Ive used Ubuntu12.04. Infact its End of Life date is 3 days away ;) Can you please send me the command and the log file which gives the exact error. Thanks. -Zeke On 04/25/2017 01:49 PM, Corinna Bauer wrote: > Hi Zeke, > > I am also having this same problem.

Re: [Freesurfer] mri_cvs_register failure from missing shared lib

Hi Zeke, I am also having this same problem. Even after completing the steps you listed above. I am running Ubuntu 12.04. Any suggetions? Thanks On Wed, May 28, 2014 at 1:50 PM, Z K wrote: > You will need to install libboost v1.41 onto your system. You should be > able to install it using yum

Re: [Freesurfer] mri_cvs_register error : PETSC Error

At the moment, unfortunately, not as the high resolution morphs are very large. Lilla On Mon, 20 Feb 2017, Bhavana Ganesh wrote: Hi Lilla, Is there a work around for this because I would at max be able to allocate 8GB for the tool but I dont have the resource for 35GB. Regards, Bhavana

Re: [Freesurfer] mri_cvs_register error : PETSC Error

Hi Lilla, Is there a work around for this because I would at max be able to allocate 8GB for the tool but I dont have the resource for 35GB. *Regards,* *Bhavana*

Re: [Freesurfer] mri_cvs_register error : PETSC Error

Hi Bhavana, We recommend to assign about 35GB of RAM on our cluster nodes for this operation. I am not sure how that compares to your VB. Lilla On Mon, 20 Feb 2017, Bhavana Ganesh wrote: Hi Lilla, I have allocated 40GB for my VB and 3GB of RAM space. I am not allocating anything specific

Re: [Freesurfer] mri_cvs_register error : PETSC Error

Hi Lilla, I have allocated 40GB for my VB and 3GB of RAM space. I am not allocating anything specific to the function. *Regards,* *Bhavana*

Re: [Freesurfer] mri_cvs_register error : PETSC Error

Hi Bhavana, How much memory are you allocating to this process? Lilla On Mon, 20 Feb 2017, Bhavana Ganesh wrote: > Hi Developers, > > I'm receiving this error while I try to run mri_cvs_register. The same error > was received when I reran the same even after increasing the memory allocated

Re: [Freesurfer] mri_cvs_register: how to read/import .m3z warp file

Hi Stefano, You can try to use the attached matlab file for reading the m3z file. Lilla On Mon, 30 Jan 2017, Stefano Zappalà wrote: Dear FreeSurfer Developers, I am trying to visualize and modify the output warp field (in .m3z) of a mri_cv_registration call aimed at aligning a T1w scan to

[Freesurfer] mri_cvs_register: how to read/import .m3z warp file

Dear FreeSurfer Developers, I am trying to visualize and modify the output warp field (in .m3z) of a mri_cv_registration call aimed at aligning a T1w scan to the MNI space. I was wondering how file format .m3z is organized, in order to read it with, for example, matlab. Or if there are simpler

Re: [Freesurfer] mri_cvs_register

Hi Nazanin, You need to run the full recon on your subject before you can use this registration command. Lilla On Sat, 24 Dec 2016, N Saf wrote: Dear Freesurfers, I try to register my subject with cvs atlas in mni space I use this command mri_cvs_register --mov subject.nii --mni I got this

[Freesurfer] mri_cvs_register

Dear Freesurfers, I try to register my subject with cvs atlas in mni space I use this command mri_cvs_register --mov subject.nii --mni I got this error: Using m3z type morph files. amir : at least one mean and/or Gaussian curvature file is missing (.H, .K) /home/nazanin/freesurfer/subjects/amir/s

Re: [Freesurfer] mri_cvs_register quit for mris_resample: Command not found

Ok this is a known issue with the freesurfer-Darwin-lion-stable-pub-v5.3.0 release. Please download a copy of mris_resample from the following link and copy it into your FREESURFER_HOME/bin directory. Also, make sure it is executable (chmod +a mris_resample) ftp://surfer.nmr.mgh.harvard.edu/

Re: [Freesurfer] mri_cvs_register quit for mris_resample: Command not found

Hi Z K The contents of build-stamp.txt are freesurfer-Darwin-lion-stable-pub-v5.3.0. Best Wishes Cong Chen > Date: Tue, 18 Oct 2016 11:09:20 -0400 > From: Z K > > > Hello, > > Can you provide me with the contents of your > /Applications/freesurfer/build-stamp.txt file? > > > > On 10

Re: [Freesurfer] mri_cvs_register quit for mris_resample: Command not found

Hello, Can you provide me with the contents of your /Applications/freesurfer/build-stamp.txt file? On 10/18/2016 10:13 AM, Cong wrote: > Dear freesufer experts > I’m learning DTI image process according to steps in FsTutorial/ > Diffusion_DtiIntegration. In Spatial Normalization I need cr

[Freesurfer] mri_cvs_register quit for mris_resample: Command not found

Dear freesufer experts    I’m learning DTI image process according to steps in  FsTutorial/ Diffusion_DtiIntegration. In Spatial Normalization I need create a .m3z morph file through mir_cvs_register. I used command mri_cvs_register --mov subjectname --template cvs_avg35. But it always stop for mri

Re: [Freesurfer] mri_cvs_register : output

Hi Elijah, Yes, it is. Lilla On Sun, 20 Mar 2016, Elijah Mak wrote: Hi Freesurfer Community, I am running mri_cvs_register for the spatial normalization and it seems to work very nicely on my set of DTI data in subjects with substantial atrophy.  However, I can't seem to find the file  co

[Freesurfer] mri_cvs_register : output

Hi Freesurfer Community, I am running mri_cvs_register for the spatial normalization and it seems to work very nicely on my set of DTI data in subjects with substantial atrophy. However, I can't seem to find the file combined_tocvs_avg35_elreg_afteraseg-norm.m3z, however, I have final_CVSmorph_to

Re: [Freesurfer] mri_cvs_register using high resolution images

I have a .dat file that I tried to pass using the --reg flag. It changed the position of the normalized high res output, but it is still not on the template. When I run mri_info on this high-resolution images, this is the output: type: nii dimensions: 408 x 510 x 537 voxel sizes:

Re: [Freesurfer] mri_cvs_register using high resolution images

Oh, I see you do not have a recon for your high res volume. Could you try the below mri_vol2vol command with an additional -lta flag that has the transform that you computed to align your lowres and high res volumes? Lilla On Wed, 6 May 2015, Celine Louapre wrote: > Thank you Lilla for the sugg

Re: [Freesurfer] mri_cvs_register using high resolution images

Thank you Lilla for the suggestion. You mean that I should run mri_cvs_register on the high res volume, is that correct? In that case, how can I specify the input volume? I did not find in the --help a way to specify manually the file to be registered, just the subject id. Thank you again Celine >

Re: [Freesurfer] mri_cvs_register using high resolution images

Hi Celine, The m3z morph encodes a sptial transformation between two particular coordinate systems. When you use mri_vol2vol below, the original space is not the same as for your input volume used to be and that is why the volumes are not in correspondence. Could you compute the registration

[Freesurfer] mri_cvs_register using high resolution images

Hi Freesurfer experts I am planing to do a voxelwise group analysis from images acquired at 7T, and I wanted to use the mri_cvs_register script, which gives very nice normalization outputs. I was wondering how to adapt the script to images that we have with 0.33mm isotropic resolution, and which ar

Re: [Freesurfer] mri_cvs_register

Could you also send the log file along? Thanks, Lilla On Wed, 10 Sep 2014, bigben2...@web.de wrote: > I'm using the version stable v5.3.0. > Ben > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/li

Re: [Freesurfer] mri_cvs_register

Hi Ben, What version of freesurfer are you using? Lilla On Wed, 10 Sep 2014, bigben2...@web.de wrote: Hey everyone,   i have tried to run the mri_cvs_register command but it returned an error in the second step. It returned:   "VolumeMorph load - failed to open input stream"   I have entere

[Freesurfer] mri_cvs_register

Hey everyone,   i have tried to run the mri_cvs_register command but it returned an error in the second step. It returned:   "VolumeMorph load - failed to open input stream"   I have entered: "mri_cvs_register --mov sub1 --template sub2" What could i do to fix it?   Thanks for your help  

Re: [Freesurfer] mri_cvs_register failure from missing shared lib

You will need to install libboost v1.41 onto your system. You should be able to install it using yum: $>yum install boost-devel However, its possible that the version you get thru this method may be incompatible with the version required by freesurfer. If the above does not fix your issue, the

[Freesurfer] mri_cvs_register failure from missing shared lib

Hi, I had mri_cvs_register die on me when it couldn't find a shared library. Relevant bit is (full log is attached): mris_resample: error while loading shared libraries: libboost_program_options.so.5: cannot open shared object file: No such file or directory Freesurfer bugr info: ---

Re: [Freesurfer] mri_cvs_register for EPI

Thank you Lilla, this explains my case. The accuracy of mri_cvs_register is legendary and incorporating this into standard fMRI processing pipeline is most desirable:) Could you please inform the group once this feature is implemented? Thank you! Best regards, Marcel 2013/8/8 Lilla Zollei > >

Re: [Freesurfer] mri_cvs_register for EPI

Hi Marcel, We have encountered this problem before, but we have not come up with the perfect solution yet. As you dais, either the volume gets resampled twice or the high res tranformation needs to be downsampled. Neither of these is ideal, but I am planning on implementing applying the morph

Re: [Freesurfer] mri_cvs_register for EPI

Hello Lilla, thank you the clarifications. I managed to get mri_vol2vol running, but I have one remaining obstacle - when I use the CVS template as target volume, the EPIs get resampled to 1mm isotropic voxels. I need to get a 3x3x3mm resolution. I tried to use mri_convert -vs 3 3 3 norm.mgz norm3

Re: [Freesurfer] mri_cvs_register for EPI

Hi Marcel, First, you will find a lot of details about the usage of mri_cvs_register if you use the --help flag in the terminal. See detailed responses to your questions below:  I'm trying to use mri_cvs_register (whose registration accuracy is, by the way, jaw-dropping) for EPI images. Ho

[Freesurfer] mri_cvs_register for EPI

Hello, I'm trying to use mri_cvs_register (whose registration accuracy is, by the way, jaw-dropping) for EPI images. However, the descriptions which I've found on the web do not make the task easier. My goal is to get functional images in cvs_avg35_inMNI152 space, resampled to 3mm isotropic resolu

Re: [Freesurfer] mri_cvs_register std:: bad_alloc

Hi Lilla, thanks for the advice, I'll just upgrade my RAM to 24 GB (maybe it will help FSFAST too ;-)). I used the --m3d flag as a blind guess about the possible cause of the aforementioned error, thank you for clearing that up, I'll skip it next time. Best regards, Marcel 2013/7/9 Lilla Zolle

Re: [Freesurfer] mri_cvs_register std:: bad_alloc

Hi Marcel, You would ned at least twice as much. Also, is there a specific reason for you to use the --m3d flag? That will result in writing out uncompressed morph files which will take up a lot of space. Lilla On Tue, 9 Jul 2013, Marcel Falkiewicz wrote: Dear FreeSurfers,  I'm trying to us

[Freesurfer] mri_cvs_register std:: bad_alloc

Dear FreeSurfers, I'm trying to use mri_cvs_register, however the process can't complete and I get the following error: [...] loading transform id string = data size = 18728074 uilen = 6 loading transform id string = data size = 19845421 uilen = 6 loading transform id string = data size = 1

Re: [Freesurfer] mri_cvs_register - use of wmparc instead of aseg

Hi Daniel. > i'm currently applying mri_cvs_register and I'm very happy with the nice > results. Congratulation for this very clever approach. However, some data > sets which I work on have still aseg.mgz which are not segmented > appropriately. As far as I understand aseg.mgz is not redefined

[Freesurfer] mri_cvs_register - use of wmparc instead of aseg

Dear Lilla, i'm currently applying mri_cvs_register and I'm very happy with the nice results. Congratulation for this very clever approach. However, some data sets which I work on have still aseg.mgz which are not segmented appropriately. As far as I understand aseg.mgz is not redefined after e

Re: [Freesurfer] mri_cvs_register error in step 2

Hi Jackie, Sorry that the error is still there. Are you sure that the attached log file is for the below command? I am asking as the log file indicates that spherical registration is done and that should not happen in Step2. Also, could you tell me which version of the FS distribution you ar

Re: [Freesurfer] mri_cvs_register error in step 2

hi Lilla, I ended up with the same error... so I'm not sure what else to try. Do you have an ideas for troubleshooting? I've also attached the latest log file, although it's probably very similar to the first one. thanks, jackie On Fri, Apr 20, 2012 at 6:10 PM, Jackie Leung < jackie.le...@alu

Re: [Freesurfer] mri_cvs_register error in step 2

The files in the folder are around 4.7MB... and 2 .annot files that are around 1Mb. I am able to open these surface files using Freeview. Like I said before, I tried copying and surf2vol command line and running it separately, and this error won't appear. In contrast, if i run mri_cvs_register -

Re: [Freesurfer] mri_cvs_register error in step 2

Hi Jackie, What is the size of the *resample* files? The only thing I can think about is that the files are corrupted and the code cannot read those files in. You could try to read the resampled files into Freeview, to test whether they can be opened or you could delete the files and then the

Re: [Freesurfer] mri_cvs_register error in step 2

ok... please see attached. note: The directory name is different in this log file, but the error is the same. I've been testing this problem with many different directories. thanks, jackie On Thu, Apr 19, 2012 at 5:37 PM, Lilla Zollei wrote: > > Hi Jackie, > > Could you attach the log file? >

Re: [Freesurfer] mri_cvs_register error in step 2

Hi Jackie, Could you attach the log file? Thanks, Lilla On Thu, 19 Apr 2012, Jackie Leung wrote: hi, I'm trying to run mri_cvs_register and I'm getting a strange error message.  MRISread(CVS_test_26to47_1/lh.resample.white): could not open file No such file or directory  Error reading surf

[Freesurfer] mri_cvs_register error in step 2

hi, I'm trying to run mri_cvs_register and I'm getting a strange error message. MRISread(CVS_test_26to47_1/lh.resample.white): could not open file No such file or directory Error reading surface CVS_test_26to47_1/lh.resample.white I've checked the directory and the file definitely exists. It s

Re: [Freesurfer] mri_cvs_register on a 64-bit Mac crash PETSC ERROR

Hi Rey, We are working on a 64 bit Mac version, but don't quite have one yet Cheers Bruce On Mar 5, 2012, at 6:36 PM, Rey Ramirez wrote: > Dear colleagues, especially Lilla Zollei, > > I am trying to run mri_cvs_register on a 64-bit Mac but it crashes at the > same place where other people h

Re: [Freesurfer] mri_cvs_register error on Mac

Hi Peter, Could you attach the log files from your process? Lilla On Mon, 5 Dec 2011, Peter J. Molfese wrote: > All, > > I've been trying to use mri_cvs_register on a 64-bit mac and received the > following error (below). Google found a couple of hits that others are > having this problem b

[Freesurfer] mri_cvs_register error on Mac

All, I've been trying to use mri_cvs_register on a 64-bit mac and received the following error (below). Google found a couple of hits that others are having this problem but no solution. I'm running the most recent version from version 5.1 with the patch on the release notes page ($Id: mri_cv

Re: [Freesurfer] mri_cvs_register can not find

Hi Lilla, it seems that my linux system was not in consistent state. After running some sanity checks and repairing some findings, the mri_cvs_register is able to continue beyond the point where it used crashed before. Thanks, Martin On Fri, Nov 4, 2011 at 12:40 PM, wrote: > Hi Martin, > Coul

Re: [Freesurfer] mri_cvs_register can not find

Hi Lilla, I am using v 1.15.2.9 on 64-bit Gentoo Linux running inside vmware virtual machine with 15GB of allocated RAM and 4 cores. I can share also the log file, but it will take a while to get it out of the vmware VM. I will send it later today. Thanks a lot and best regards, Martin On Fri,

Re: [Freesurfer] mri_cvs_register can not find

Hi Martin, Could you give more details? Which version of mri-cvs-register are you using? Was there a log file that you could share also? Thanks, Lilla --Original Message-- From: Martin Kavec To: Freesurfer mailing list To: Lilla Zollei Subject: mri_cvs_register can not find Sent: Nov 4, 20

[Freesurfer] mri_cvs_register can not find

Hi all, I am trying to run mri_cvs_register but for some reasons it always terminates with: ERROR: Can not find or read $SUBJECTS_DIR/MY_SUBJECTS/cvs/combined_tocvs_avg35__elreg_aseg.m3z My command is as follows: mri_cvs_register --mov MY_SUBJECT Indeed the file is not there, but another one w

Re: [Freesurfer] mri_cvs_register version for CentOS4 and CentOS5

Hi, Yes, you should. Lilla On Sat, 11 Jun 2011, t...@ms36.hinet.net wrote: >

Dear FS experts

>

I download CentOS5 x86-64 version (not CentOS4) of FS 5.1. should I > need to upgrade the mri_cvs_register and applyMorph for correction ?

>

best

>

JLH

__

Re: [Freesurfer] mri_cvs_register update

34 -0400 (EDT) >> From: Lilla Zollei >> Subject: [Freesurfer] mri_cvs_register update >> To: freesurfer@nmr.mgh.harvard.edu >> Message-ID: >> >> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed >> >> >> Hi, >> >> W

[Freesurfer] mri_cvs_register version for CentOS4 and CentOS5

Dear FS experts

I download CentOS5 x86-64 version (not CentOS4) of FS 5.1. should I need to upgrade the mri_cvs_register and applyMorph for correction ?

best

JLH

___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https:

Re: [Freesurfer] mri_cvs_register update

la Zollei > Subject: [Freesurfer] mri_cvs_register update > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: > > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > > Hi, > > We found a bug in the mri_cvs_register script after the > release. Please,

[Freesurfer] mri_cvs_register update

Hi, We found a bug in the mri_cvs_register script after the release. Please, download the new version of applyMorph and mri_cvs_register from one of the below links for Linux Centos4, Linux Centos4 x86 64 and Mac Leopard respectively: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/l