[Freesurfer] Area after fsaverage resample

Dear FreeSurfer Developers I have a question regarding the area measures for subjects following registration to fsaverage (produced through the qcache flag – lh/rh.area.fsaverage.mgh). What do the values for each vertex represent? Is it correct to state that these measures are in mm2, or are t

[Freesurfer] aparcstats2table

Hi everyone, I am trying to use following command to save stats from a set of subjects in a table format: aparcstats2table --qdec qdec.dat --hemi lh --meas thickness -t zzz.txt But after I run this, I get following error: Traceback (most recent call last): File "/usr/local/freesurfer/bin/apa

Re: [Freesurfer] GM ROI list?

OK, thanks for that list of complementary ROIs. I've always wondered what is the maximal set of regions that can be returned by the standard recon-all with no other options for aparc+aseg and aparc+aseg2009? Looking at the FreeSurferColorLUT.txt, I guess there is a batch from lines 1-231 (spannin

[Freesurfer] Longitudinal Stream on HCP Data

Aww thank you for clarifying Michael. I definitely misread Matthew's post. -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Mobile: 507-259-3434 (texts okay) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mai

[Freesurfer] Fwd: [HCP-Users] HCP to FreeSurfer Resampling

FreeSurfer experts, I am attempting to resample HCP data into FreeSurfer space with the following how to document: https://wiki.humanconnectome. org/display/PublicData/HCP+Users+FAQ. I believe I have resampled the GIFTI file into

Re: [Freesurfer] mapping ROI to surface space

hou could do it easily enough in matlab with read_label.m and write_wfile.m, but as Doug says, w files are a goofy format that we never use anymore. On Tue, 8 Nov 2016, Douglas Greve wrote: Not sure. We are trying to get away from .w files for this reason. Can you use something other than a

Re: [Freesurfer] mapping ROI to surface space

Not sure. We are trying to get away from .w files for this reason. Can you use something other than a w file? On 11/8/16 12:35 PM, Andrews, Derek wrote: > Thank you Doug that worked perfectly. > > Is it possible then to go back to a .w from a label? > > >

Re: [Freesurfer] GM ROI list?

Actually, what it does is to binarize all the labels that it thinks are not GM, and then invert the mask to give GM. for what it is worth, there are the non-GM numbers MatchValues[nMatch++] = 2; MatchValues[nMatch++] = 41; MatchValues[nMatch++] = 77; MatchValues[nMatch++]

Re: [Freesurfer] GM ROI list?

OK. But going back to my question that kicked this thread off, actually what I was looking for was just such a rule. I could make a fairly solid list of GM from using this new "mri_binarize --gm " on several recon-all outputs. Would it be possible to have the rule (presumably a list of numbe

Re: [Freesurfer] mapping ROI to surface space

use mri_label2label with the --outmask option On 11/8/16 12:37 PM, Andrews, Derek wrote: > Apologies I meant from a label to a .mgh > > Best, Derek > > > > Derek Sayre Andrews, MSc > PhD Candidate > > The Sackler Institute for Translational Neurodevelopmen

Re: [Freesurfer] mapping ROI to surface space

Apologies I meant from a label to a .mgh Best, Derek Derek Sayre Andrews, MSc PhD Candidate The Sackler Institute for Translational Neurodevelopment Department of Forensic and Neurodevelopmental Sciences Institute of Psychiatry, Psychology & Neuroscienc

Re: [Freesurfer] mapping ROI to surface space

Thank you Doug that worked perfectly. Is it possible then to go back to a .w from a label? Derek Sayre Andrews, MSc PhD Candidate The Sackler Institute for Translational Neurodevelopment Department of Forensic and Neurodevelopmental Sciences Institute of

Re: [Freesurfer] GM ROI list?

Yes. It just uses a rule on the numbers that it expects to be GM. At some point, I'll add both tissue type and laterality info to the ROIs, but not for version 6 On 11/8/16 12:03 PM, P Taylor wrote: And a final question, which might be a silly one-- This GM map applies to both the aparc.a200

[Freesurfer] MP2RAGEs

hi there, will FS 6.0 have any special options for MP2RAGE sequences? specifically i'm trying to decide whether to collect MPRAGE or MP2RAGE T1s; either would be at 0.7mm iso (7T data). i've heard skull-stripping is the main issue with the MP2RAGE and so i'm curious if FS 6.0 will have any adap

Re: [Freesurfer] GM ROI list?

And a final question, which might be a silly one-- This GM map applies to both the aparc.a2009s+aseg.mgz and aparc+aseg.mgz files, right? Running "mri_binarize --gm ..." on each of those files separately gave the same mask-- I believe this should be a general property? Thanks, pt On Tue, Nov 8,

Re: [Freesurfer] GM ROI list?

yes On 11/8/16 11:51 AM, P Taylor wrote: Ah, cool, that looks like it does the trick-- thanks much. Will that version of mri_binarize be in the next release of FS? Thanks, pt On Tue, Nov 8, 2016 at 11:35 AM, Douglas Greve mailto:gr...@nmr.mgh.harvard.edu>> wrote: Try this one ht

Re: [Freesurfer] GM ROI list?

Ah, cool, that looks like it does the trick-- thanks much. Will that version of mri_binarize be in the next release of FS? Thanks, pt On Tue, Nov 8, 2016 at 11:35 AM, Douglas Greve wrote: > Try this one https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_binarize > > On 11/8/16 11:26 AM, P

Re: [Freesurfer] GM ROI list?

Try this one https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_binarize On 11/8/16 11:26 AM, P Taylor wrote: Thanks, I'd like to try that. However, my mri_binarize doesn't show that option, and when I try running it, that option isn't recognized: $ mri_binarize --gm --o map_gm.nii --i apa

Re: [Freesurfer] GM ROI list?

Thanks, I'd like to try that. However, my mri_binarize doesn't show that option, and when I try running it, that option isn't recognized: $ mri_binarize --gm --o map_gm.nii --i aparc+aseg.mgz ERROR: Option --gm unknown Looking at the mri_binarize help, I see '--wm' exists, and that does, indeed,

Re: [Freesurfer] Longitudinal Stream on HCP Data

yes, thanks Mike, that is true as well. The new V6 works very nicely on data that is higher res than 1mm On Tue, 8 Nov 2016, Harms, Michael wrote: To clarify, in that post, Matt wasn’t saying that FS was going to incorporate myelin maps.  Rather, the new (v6) version of FS, with its support of

Re: [Freesurfer] Fw: recon-all steps question

The brainmask.auto.mgz will be our stripping, but the brain,ask.mgz will be yours Cheers Bruce > On Nov 8, 2016, at 10:21 AM, miracoo...@gmail.com wrote: > > Thank you very much Bruce. Last questions. When I replace FS generated > brainmask.mgz with mine, does the original also remain in the m

Re: [Freesurfer] Longitudinal Stream on HCP Data

Hi Tim for a long time we have had a post-processing routine that uses T2 or FLAIR images for post-hoc surface deformation. This existed long before the HCP, although I did tweak it for the Wash U HCP acquisition to make it perform better. The upcoming v6 has the overall best performance with t

Re: [Freesurfer] mapping ROI to surface space

Use mri_surf2surf to convert it to an mgh or mgz file, then use mri_cor2label with the --surf option to convert it to a label On 11/8/16 9:41 AM, Andrews, Derek wrote: > Hi Bruce and Freesurfer developers, > > Thank you. Any suggestions on converting a binary .w file to a label would > be very h

Re: [Freesurfer] GM ROI list?

We don't currently have that information (ie, tissue type) stored with the ROI. One thing you can do is to run mri_binarize with the --gm option on aparc+aseg.mgz This uses some rules to determine what is GM and creates a mask of GM. You can then feed this into mri_segstats with --mask, and i

Re: [Freesurfer] perl & bbregister conflicts

fyi: the new version of bbregister will use the FS-native mri_coreg, so this problem will disappear On 11/8/16 10:17 AM, Z K wrote: > Thank you for this information. I believe we test against the same > version of fsl (5.0.7). I'll look into it. > > On 11/08/2016 06:32 AM, GREGORY R KIRK wrote:

Re: [Freesurfer] Longitudinal Stream on HCP Data

To clarify, in that post, Matt wasn’t saying that FS was going to incorporate myelin maps. Rather, the new (v6) version of FS, with its support of data acquired with < 1 mm resolution, may eliminate the need for some of the steps that are currently the HCP Pipelines that are there to take full

Re: [Freesurfer] Fw: recon-all steps question

Thank you very much Bruce. Last questions. When I replace FS generated brainmask.mgz with mine, does the original also remain in the mri folder( that's having 2 brainmask.mgz)  or  is the original permanently replaced with my own brainmask.mgz ( that's only 1 brainmask.mgz which is mine)? Second

Re: [Freesurfer] perl & bbregister conflicts

Thank you for this information. I believe we test against the same version of fsl (5.0.7). I'll look into it. On 11/08/2016 06:32 AM, GREGORY R KIRK wrote: > Hi folks, > > > somebody stuck me with Ubuntu 16 for a month > > and I found the perl problem and so switched to > > the dev version which

[Freesurfer] Longitudinal Stream on HCP Data

Hi Freesurfer/HCP experts, I am curious if there is a way to incorporate HCP data (i.e. myelin maps) into the FreeSurfer processing stream. Matthew Glasser mentioned in a post on the HCP mailing list about a month back that this is being actively worked on by FreeSurfer: http://www.mail-archive.co

Re: [Freesurfer] FreeSurfer Dev Releases

On 11/07/2016 05:39 AM, Elia S. wrote: > Dear FreeSurfer Developers, > > > We have been trying out, for the past few months, the freesurfer dev > releases, and in particular this one: > > > freesurfer-X86_64-unknown-linux-gnu-dev5-20150924 > > > My question is, does the above version classify as

Re: [Freesurfer] mapping ROI to surface space

Hi Bruce and Freesurfer developers, Thank you. Any suggestions on converting a binary .w file to a label would be very helpful. Best, Derek Derek Sayre Andrews, MSc PhD Candidate The Sackler Institute for Translational Neurodevelopment Department of Fo

Re: [Freesurfer] FW: Manual pial and white matter corrections cause irregularities

Hi Cleo to check I need the actual subject directories. Can you tar, gzip and upload the before and after ones? cheers Bruce On Tue, 8 Nov 2016, Cleo Vandervost wrote: Hi Bruce; Sorry to send this email once again but I didn't get an answer to my previous one. As you asked, I upload

Re: [Freesurfer] mapping ROI to surface space

Hi Derek I'll cc the FS list so others can answer. It depends on the reason the holes exist. It also depends on the size of the holes. The dev version of mri_label2labels supports morphological close operations. It takes an integer parameter which should be about the radius of the holes you w

[Freesurfer] perl & bbregister conflicts

Hi folks, somebody stuck me with Ubuntu 16 for a month and I found the perl problem and so switched to the dev version which solved that problem. discovered that with the dev version bbregister throws an error having to do with fsl flirt throws an error `terminate after throwing an instanc