Re: [Freesurfer] possible to use multiple B value DTI in Tracula?

Hi, did you try specifying values in bvals file? (set bvalfile=... ) Riccardo Salil Soman salso...@stanford.edu ha scritto: Hi, I was wondering - is it possible to use DTI data of multiple B values in Tracula (acquired during the same session and same TE)? Best wishes, Sal Salil Soman,

[Freesurfer] error with fast_selxavg3

Hi, I am running into an error with fast_selxavg3 (NaN values in XtX). Other have people reported similar problems on the mailing list and I've tried implementing some of the suggestions (namely, using -nowhiten and checking that all events exist in my paradigm file), but I can't get rid of

Re: [Freesurfer] bvecs error from Tracula

Dear Anastasia, I am trying to download the dmri_5.1_snow_leopard.tar.gzftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-snow-leopard-intel/dmri_5.1_snow_leopard.tar.gz from FreeSurfer website to solve memory problem but it is not available. Would you please check the source to the

[Freesurfer] Average cortical diffusion

Hi, I've registered the mean diffusivity (MD) values on the cortical surface. Can you please tell me how to get the average cortical MD of the whole hemisphere for each subject, rather than the regional cortical MD. Kind regards, Afaf This message and any attachment are intended solely for

Re: [Freesurfer] Average cortical diffusion

use mri_vol2surf to sample it onto the surface, then give mris_anatomical_stats the file that it created instead of thickness (-t file name). Everthing it reports as thickness will actually be MD values instead On Mon, 22 Jul 2013, Afaf Elsarraj wrote: Hi,   I’ve registered the mean

[Freesurfer] freeview save error

Hi there, Occassionally when using the save volume function from the gui to save edits made to the wm.mgz, freeview crashes (see command line error report below) and the wm.mgz being deleted from subject's 'mri' directory (the temp wm.mgz~ is still present...but all edits are lost). I am running

Re: [Freesurfer] freeview save error

Hi Jason any chance you can figure out how to replicate this reliably? If so, we can track it down. Otherwise it's going to be hard thanks Bruce On Mon, 22 Jul 2013, Jason Tourville wrote: Hi there,Occassionally when using the save volume function from the gui to save edits made to the

[Freesurfer] [Tracula] Run trac-all with 2 time points for DTI scan but 1 time point for T1 scan. How to?

Hi, I need to run trac-all on subjects scanned first time in T1 and DTI, second time DTI only. How to configure dmrirc? I've seen long.example but it seems that it require T1 second run too. Tnx, Riccardo ___ Freesurfer mailing list

Re: [Freesurfer] Recon-all difficulties off-site

Hi Michelle is the MNI stuff installed? If seems like ti can't find MNI/Startup.pm. Mine is under: $MNI_PERL5LIB/MNI/Startup.pm cheers Bruce On Sun, 21 Jul 2013, Michelle W. Voss wrote: Hi, I seem to be having the same error, recon all is crashing out with the mri_nu_correct.mni

Re: [Freesurfer] Skull stripped MNI305

Try $SUBJECTS_DIR/fsaverage/mri/brain.mgz doug On 07/19/2013 03:06 PM, Fotiadis, Panagiotis wrote: Hi, I was wondering if there is a skull stripped version of the file /usr/local/freesurfer/stable5_0_0/average/mni305.cor.mgz stored anywhere. I tried applying bet and mri_watershed on the

Re: [Freesurfer] Average cortical diffusion

Many thanks From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: 22 July 2013 16:31 To: Afaf Elsarraj Subject: RE: [Freesurfer] Average cortical diffusion can you cc the list so that others can answer and learn from the responses? Put -t MD sampled to

[Freesurfer] rtview

Dear Freesurfer Users, I am running a retinotopic analysis in the 5.1.0 version of freesurfer. As tksurfer is not ideal for viewing the retinotopic data, I have been trying to find a download for rtview. I tried to go to the following link:

Re: [Freesurfer] autorecon2-wm without mri_fill in v4.5?

I guess the solution is -nofill... 2013/7/20 Caspar M. Schwiedrzik cschwie...@rockefeller.edu: Hi Freesurfer Experts, I am working on a primate anatomy and I am having problems with the white matter filling in the temporal lobe in version 4.5. I manually edited wm.mgz and recreated

Re: [Freesurfer] rtview

Sorry, try now On 07/22/2013 12:28 PM, Nicholas Paul Denisuk wrote: Dear Freesurfer Users, I am running a retinotopic analysis in the 5.1.0 version of freesurfer. As tksurfer is not ideal for viewing the retinotopic data, I have been trying to find a download for rtview. I tried to go to

Re: [Freesurfer] error with fast_selxavg3

Hi Leila, does it work if you change the -refeventdur to something larger (eg, 2)? doug On 07/22/2013 06:11 AM, Leila Reddy wrote: Hi, I am running into an error with fast_selxavg3 (NaN values in XtX). Other have people reported similar problems on the mailing list and I've tried

Re: [Freesurfer] possible to use multiple B value DTI in Tracula?

Thank you. I can concatenate the 3 acquisitions (I have 1 b2500, and 2 b1000) into a single nifti file, and then arrange the bval and bvec files to match. I will give it a try. Thank you for all your help. Best wishes, Sal On Mon, Jul 22, 2013 at 11:11 AM, Anastasia Yendiki

Re: [Freesurfer] bvecs error from Tracula

Hi Amirhossein - That fix applied only to the 5.1 version. I'd recommend using the 5.3 version for tracula. Are you getting a memory error, and if so with which version? Thanks, a.y On Mon, 22 Jul 2013, amirhossein manzouri wrote: Dear Anastasia,  I am trying to download the 

Re: [Freesurfer] possible to use multiple B value DTI in Tracula?

Hi Sal - Are these different scans that you want to merge? If they're all in one file, then you just define the b-value for each frame as usual in the bvalfile. There's no rule that all the b-values have to be the same. Hope this helps, a.y On Sun, 21 Jul 2013, Salil Soman wrote: Hi, I was

Re: [Freesurfer] [Tracula] Run trac-all with 2 time points for DTI scan but 1 time point for T1 scan. How to?

Hi Riccardo - The way this is designed is that you have to have longitudinal T1 data and run the longitudinal stream of recon-all on it, before you run the longitudinal version of tracula on your DWI. You could fake this by simply creating a copy of the recon-all directory of your first T1

[Freesurfer] mri_label2label ERROR: srcvtxno=-1

Dear Freesurfer list, I was converting a surface label from 'fsaverage' space to individual subjects and got this error: ###-### Performing mapping from target back to the source label ERROR: srcvtxno = -1 0 trgvtxno = 140122, dmin = 1000 trgregxyz = 0, 0, 0 This means that

[Freesurfer] recon-all error

Hi everyone, I'm quite new to FreeSurfer, my apologies for asking the obvious. I tried to run recon-all on multi echo T2* weighted data and got the following error: 'input(s) cannot have multiple frames' I was wondering how I should go about running recon-all on multi echo data. Any help

Re: [Freesurfer] Recon-all difficulties off-site

The MNI directory directly under freesurfer is there, but the MNI_PERL5 directory is not. e.g, bash-3.2$ echo $MNI_PERL5LIB /Applications/freesurfer/mni/lib/../System/Library/Perl/5.8.6 bash-3.2$ cd $MNI_PERL5LIB bash: cd: /Applications/freesurfer/mni/lib/../System/Library/Perl/5.8.6: No such file

Re: [Freesurfer] recon-all error

we need a T1-weighted input, such as FLASH (with flip angle =20deg) or mprage cheers Bruce On Mon, 22 Jul 2013, Smian wrote: Hi everyone, I'm quite new to FreeSurfer, my apologies for asking the obvious. I tried to run recon-all on multi echo T2* weighted data and got the following

Re: [Freesurfer] bvecs error from Tracula

Hi, Yes I am getting the memory error with version 5.3, exactly the one that is reported in this link: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-July/019392.html Thanks, On Mon, Jul 22, 2013 at 8:15 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Amirhossein -

Re: [Freesurfer] Skull stripped MNI305

Thanks Doug, that looks great! In addition, is the specific fsaverage brain in the MNI space? Panos 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:

Re: [Freesurfer] Skull stripped MNI305

yes, mni305 doug On 07/22/2013 04:28 PM, Fotiadis, Panagiotis wrote: Thanks Doug, that looks great! In addition, is the specific fsaverage brain in the MNI space? Panos From: freesurfer-boun...@nmr.mgh.harvard.edu

Re: [Freesurfer] Skull stripped MNI305

Great, thanks! 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: Monday, July 22, 2013 4:46 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer]

Re: [Freesurfer] mri_label2label ERROR: srcvtxno=-1

what is the input label? How was it created? Does it have -1 as the first number on any line? On 07/22/2013 03:54 PM, Lingqiang Kong wrote: Dear Freesurfer list, I was converting a surface label from 'fsaverage' space to individual subjects and got this error: ###-###

Re: [Freesurfer] infant atlas segmentation

Hi Mark, I have no idea what you are doing. Can you send a command line? Are either of the images generated by FS? doug On 07/22/2013 03:56 PM, Mark Plantz wrote: Hello FreeSurfers, I recently obtained a set of infant templates. Out of curiousity, I decided to view one of the input

Re: [Freesurfer] mri_label2label ERROR: srcvtxno=-1

The input label is one from a set published 1000 brain functional connectivity label from the Buckner lab (Yeo Krienen, et al., 2011). No. The first number of all lines are integers ranging from 5 to 132000. Just adding some details: 1) when we first ran recon did the same label conversion and

Re: [Freesurfer] mri_label2label ERROR: srcvtxno=-1

Can you send the first 100 lines (or point me to the label on the file system)? doug On 07/22/2013 05:01 PM, Lingqiang Kong wrote: The input label is one from a set published 1000 brain functional connectivity label from the Buckner lab (Yeo Krienen, et al., 2011). No. The first number of

Re: [Freesurfer] mri_label2label ERROR: srcvtxno=-1

Yes. The label file is attached. Although since this error did not happen with the old surface of the same subject, I suspect editing it and running autorecon2-wm created a new surface that had some unknown issues. Lingqiang Can you send the first 100 lines (or point me to the label on the

Re: [Freesurfer] mri_label2label ERROR: srcvtxno=-1

Are you sure the label was generated on fsaverage? Does it look ok if you run tksurfer fsaverage lh inflated -label lh.7Networks_1.first110.label On 07/22/2013 05:13 PM, Lingqiang Kong wrote: Yes. The label file is attached. Although since this error did not happen with the old surface of

Re: [Freesurfer] mri_label2label ERROR: srcvtxno=-1

yes, spherical registration is part of autorecon3, so that makes sense On Mon, 22 Jul 2013, Lingqiang Kong wrote: Yes. The input label looks fine on fsaverage. But I just realized something. After editing the surface, I re-ran autorecon2-wm and autorecon2-cp. But never autorecon3. For it to

Re: [Freesurfer] mri_label2label ERROR: srcvtxno=-1

Yes. The input label looks fine on fsaverage. But I just realized something. After editing the surface, I re-ran autorecon2-wm and autorecon2-cp. But never autorecon3. For it to do the spherical mapping correctly, I also have to re-run autorecon3 right? I did not realize that. So I'm running