[Freesurfer] -cw256 and -hires

In the git version I'm trying to use the -hires option on an image. It initially says that I need the cw256 option to restrict the FOV to 256. I tried this but initially it did nothing and then when I edited recon-all it add -cw256 to the mri_convert command to create orig.mgz but the same

[Freesurfer] TRACULA in FreeSurfer 6.0 trac-paths error

Hi Anastasia, I am getting the following error when running trac-all –paths on all of my diffusion images using the newly updated TRACULA: *vlogin03.ls5(97)$* /work/04171/dpisner/stampede/Applications/freesurfer/bin/trac-all -no-isrunning -path -c

Re: [Freesurfer] Reviewer questions...

Dear Jerome, I think I could chime in with my opinion: The Schoemaker et al paper results are based on hippocampus/amygdala segmentations in FreeSurfer 4.4. Hippocampal subfields segmentation module from development version you used should be more precise than 4.4. version and also the

Re: [Freesurfer] surface based analysis (projfrac)

Thank you very much Doug and thank you for briniging the issue of "partial volume effect " to my attention. Kindly, I have one last question.   I found in wiki that the default values for projfrc value are between 0 and 1. Are there negative values? I mean for example "-2, -1, 0 , 1, 2 ", In

Re: [Freesurfer] Binary Mask Overlay

Use mri_surf2surf to transfer the mask from one subject to another. Because this is a binary mask, you should include --mapmethod nnf on the command line On 01/11/2017 03:43 PM, Dincer, Aylin wrote: > > Hi FreeSurfer Team, > > > I used QDEC to do a group analysis and from that I generated a

Re: [Freesurfer] error: mean: DIM must be an integer and a valid dimension / selxavg3-sess with octave

Thanks Michael. This will be in the next version On 01/11/2017 07:47 AM, Michael Schirner wrote: > Dear FreeSurfers, > > I just wanted to share a solution for an issue that can arise when running > selxavg3-sess with octave instead of Matlab. > > In fast_selxavg3.m (which is called by selxavg3)

Re: [Freesurfer] surface based analysis (projfrac)

yes, that is correct. However, understand that there might only be a difference of 1mm between those two locations, so it could easily be a partial volume effect On 01/11/2017 08:50 AM, John Anderson wrote: > Thank you Doug, > Exactly! I meant GM near the CC. > When I used "projfrac=0.5 "

Re: [Freesurfer] bbregister surfaces

the pial surface is not currently used. It is possible in the current version to use pial surface if you want to On 01/12/2017 04:35 PM, Christopher Markiewicz wrote: > Hi all, > > According to > https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg25476.html, > bbregister uses the

[Freesurfer] bbregister surfaces

Hi all, According to https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg25476.html, bbregister uses the white matter surface and cortical thickness measures to perform its registrations, though there was some possibility of using the pial surface in further releases. I just want to

[Freesurfer] Fwd: OHBM 2017 Call For Council Nominations

fyi Forwarded Message Subject:OHBM 2017 Call For Council Nominations Date: Thu, 12 Jan 2017 12:42:40 -0600 From: i...@humanbrainmapping.org Reply-To: i...@humanbrainmapping.org To: gr...@nmr.mgh.harvard.edu Dear Douglas, The OHBM Nominating Committee

Re: [Freesurfer] pial surface vs. aparc segmentation inconsistency

This is due to an inconsistency between the volume labeling and the surface placement. The volume labeling thinks those voxels are cerebellum. In the lh.aparc.stats, those voxels would be counted as parahippo. If the problem is with the volume labeling, then there is nothing you need to do as

Re: [Freesurfer] autorecon1 crash (with nu_correct).

OK, I just uploaded it via the FileDrop (and sent it to Zeke)... On Thu, Jan 12, 2017 at 4:02 AM, Z K wrote: > Could you please upload the a copy of the subject data and I'll take a > look early next week when I get back. Also, what Linux distribution are you > on?

Re: [Freesurfer] Editing annot files

Hi Martin I guess you could do it in tksurfer. This functionality hasn't been addded to freeview yet cheers Bruce On Tue, 10 Jan 2017, Martin Juneja wrote: Hi, I was wondering if there is any way to edit annot file e.g. I would like to edit lh.Yeo2011_7Networks_N1000.annot file in such a

Re: [Freesurfer] Viewing Atlas for Cortical Parcellations

Hi Tamara sorry, not easily - we have no visualization tools for the cortical atlases (*.gcs files) cheers Bruce On Thu, 12 Jan 2017, Tamara Tavares wrote: > Hello, > > I was wondering whether it is possible to view the atlases that are used to > construct the cortical surface ROIs in a

[Freesurfer] Viewing Atlas for Cortical Parcellations

Hello, I was wondering whether it is possible to view the atlases that are used to construct the cortical surface ROIs in a visualization program? Thank you in advance for your help. Best, Tamara ___ Freesurfer mailing list

[Freesurfer] Fwd: Editing annot files

-- Forwarded message -- From: Martin Juneja Date: Tue, Jan 10, 2017 at 5:32 PM Subject: Editing annot files To: Freesurfer support list Hi, I was wondering if there is any way to edit annot file e.g. I would like to edit

Re: [Freesurfer] Cannot allocate memory error

Hi Aziz freeview is the tool for visualizing the data, so use it to examine the outputs of recon-all and figure out what is causing the big defect cheers Bruce On Thu, 12 Jan 2017, Aziz Nanthaamornphong wrote: Hi Bruce, So, I  should run the freeview after got those error messages. I will

Re: [Freesurfer] Cannot allocate memory error

Hi Bruce, So, I should run the freeview after got those error messages. I will try. Thank you, Aziz. On Thu, Jan 12, 2017 at 10:32 PM, Bruce Fischl wrote: > Hi Aziz > > it will be in the subject's surf dir. You can visualize it via: > > freeview -f

Re: [Freesurfer] Cannot allocate memory error

Hi Aziz it will be in the subject's surf dir. You can visualize it via: freeview -f $SUBJECTS_DIR//surf/lh.inflated.nofix cheers Bruce On Thu, 12 Jan 2017, Aziz Nanthaamornphong wrote: Hi Bruce, How can I look at inflated.nofix as you mentioned? I think I ran recon-all for the 001.mgz

[Freesurfer] Fwd: Error of fsaverage unknown during mri_glmfit

Hello FreeSurfer Developers, I am attempting to repeat the group analysis with the tutorial data on FreeSurfer website, as described on the FsTutorial/GroupAnalysis ( https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis). But I received an error message when running the mri_glmfit

Re: [Freesurfer] Cannot allocate memory error

Hi Bruce, How can I look at inflated.nofix as you mentioned? I think I ran recon-all for the 001.mgz without other files. Best Regards, Aziz. On Thu, Jan 12, 2017 at 8:55 PM, Bruce Fischl wrote: > Hi Aziz > > yes, you ran out of RAM. That said, a defect with 66K

Re: [Freesurfer] Brighter image at baseline vs. follow up using longitudinal processing stream

Hi Tamara, that information is in the screen output: Determinant : 1.03358 also Scale = diag([ 1.0109774487584 1.0113715685396 1.0108915357302 ]) so it finds some scaling (approx 1% in each axis direction, so a total of 3%). This can happen in individual cases, but if it is

Re: [Freesurfer] Cannot allocate memory error

Hi Aziz yes, you ran out of RAM. That said, a defect with 66K vertices is pretty big - more than 1/3 of a typical surface. You should check to make sure nothing big is wrong (hemis attached, skull left around, etc). Look at the inflated.nofix surface and it should be obvious what the

Re: [Freesurfer] autorecon1 crash (with nu_correct).

Could you please upload the a copy of the subject data and I'll take a look early next week when I get back. Also, what Linux distribution are you on? > On Jan 12, 2017, at 1:55 AM, Jamie Hanson wrote: > > Hello Zeke, > > I included the terminal output error for the stable

[Freesurfer] pial surface vs. aparc segmentation inconsistency

Somehow, my earlier post is unvisible on the maillist, therefore I send it again without the attached image. Dear all, In some of our subjects the border of ctx_lh_parahippocampal (green color) is inconsistent with the border of pial surface (red color) in the sense that some small region

[Freesurfer] Cannot allocate memory error

Hi experts, I ran the command $recon-all -all -subjid 0696 I have got these error messages *CORRECTING DEFECT 46 (vertices=66623, convex hull=8931)* *Excessive topologic defect encountered: could not allocate 322592700 edges for retessellation* *Cannot allocate memory* *Linux