Re: [Freesurfer] freesurfer vs ITK build from sources on ubuntu(LUCID)

To follow up on my previous message: the FS build is not facilitated by the scarcity and incompleteness of build instructions. For example ITK, PETSC (and possibly other packages) which are not even mentioned explicitly as FS prerequisites (!) need to be installed at a (version-matching!) dev-lev

Re: [Freesurfer] recon-all script order

That's what I was thinking. Thank you ! On Wednesday, November 18, 2015, Douglas N Greve wrote: > There is not an automated way to do this. You might be able to run the > steps piecemeal by specifying the flags for each step individually > > On 11/18/2015 04:29 PM, Lauren Bystrom wrote: > > Hell

Re: [Freesurfer] recon-all script order

There is not an automated way to do this. You might be able to run the steps piecemeal by specifying the flags for each step individually On 11/18/2015 04:29 PM, Lauren Bystrom wrote: > Hello all, > I am trying to run freesurfer on a set of subjects that have tumors in > their brain. To get arou

[Freesurfer] recon-all script order

Hello all, I am trying to run freesurfer on a set of subjects that have tumors in their brain. To get around the tumor, I only want to run freesurfer on one of the hemispheres. When I use hemi -?h, freesurfer exits once it hits the other hemisphere. This is a problem because it doesn't go back to f

Re: [Freesurfer] FreeSurfer question

glad to hear it Bruce On Wed, 18 Nov 2015, Tsapanou, Angeliki wrote: Hi Bruce, Thank you for your respond. It was good that it was 'brown' but after re-running it, it was staying brown. Thankfully, after days of unsuccessful trials, I started everything from the beginning and finally it worked

Re: [Freesurfer] FreeSurfer question

Hi Bruce, Thank you for your respond. It was good that it was 'brown' but after re-running it, it was staying brown. Thankfully, after days of unsuccessful trials, I started everything from the beginning and finally it worked! Thanks, Angeliki -Original Message- From: freesurfer-boun

Re: [Freesurfer] FreeSurfer question

Hi Angeliki not sure if anyone answered, and also I'm not sure that I understand. If the cerebellum is "brown" in the aseg.mgz that is good - it should be. Is there a problem with the skull stripping that you are trying to fix? cheers Bruce On Thu, 12 Nov 2015, Tsapanou, Angeliki wrote:

[Freesurfer] malloc error running glm_glmfit-sim

Hi, I'm a new FS user just trying to run through the tutorials. In the Group Analysis tutorial, doing the multiple comparisons correction, when I run mri_flmfit-sim I get a malloc() memory corruption error. The output is below. I am running the VirtualBox Xubuntu 12.04 Freesurfer 5.3.0 version o

Re: [Freesurfer] gender as nuisance factor

Just specify gender as a factor then look at the contrasts where it says that gender is accounted for or regressed out. There is really no difference between a factor of interest and a nuisance factor, it is only a matter of interpretation On 11/18/2015 02:04 PM, Tesse, Marcello wrote: > Dear F

Re: [Freesurfer] selxavg3-sess error empty conditions in paradigm file

There is not a way to model empty conditions. The easiest thing to do is to just change another condition to say it is the missing condition. It should have little effect on the final results. On 11/18/2015 02:06 PM, Danielle Miller wrote: > Hello Freesurfer Experts, > > I am reposting this as t

[Freesurfer] Fw: gender as nuisance factor

Dear Dr, Douglas, Apology if I have written the email to you, but I am try to ask this question on FS list mailsince two days, and nobody answered me. The email sent to freesurfer@nmr.mgh.harvard.edu is below. Thank uyou very much, sorry again MARCELLO From: Tess

[Freesurfer] selxavg3-sess error empty conditions in paradigm file

Hello Freesurfer Experts, I am reposting this as this has not come up on the mail archive thread. I keep running into the following error (see below) when selxavg3-sess gets to my third subject. I am assuming this is because this subject does not have all of the conditions modeled (that is, this

[Freesurfer] gender as nuisance factor

Dear FreeSurfer experts, > > > I a PhD student at King's college London. > > I am running cortical thickness analysis with QDEC. > > I would like to investigate some cortical thickness differences > between 2 groups, > > using as nuisance factors 'age' and 'gender'. > > > No problem at all with age

Re: [Freesurfer] FSFAST First-Levels: Fast_selxavg3() ERROR

Hi Doug, Just checking up on the error below. __ Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-

Re: [Freesurfer] PET tools in FS dev v6.0

For single frame, you can just run mri_convert input.nii output.nii --frame F where F is the 0-based frame number, then run mri_gtmpvc on output.nii The PVC "image" is a bit tricky. You can get a muller-gartner image (--mgx) or region-based voxel-wise (RBV) image with --rbv. On 11/18/2015 12:3

Re: [Freesurfer] Multimodality analysis in FreeSurfer

If I understand you, you want to do a vertex-wise correlation between thickness and myelin. You can do this with a "per vertex regressor", --pvr input to mri_glmfit, something like mri_glmfit --y thickness.mgh --pvr myelin.mgh --surf fsaverage lh --C contrats.mtx --o glmdir with contrast.mtx

Re: [Freesurfer] PET tools in FS dev v6.0

Hello Doug, I am in the process of testing the FS PVC procedure and I was wondering if there is a way to do this procedure with single frame PET data and get the partial volume corrected SUVR image. I know that this is still new and not all the processes is documented yet, but any inputs on this w

[Freesurfer] Obtaining MNI-305 Coordinates for Destrieux ROIs

Hello, I was following the conversation (recreated below) about converting the Destrieux ROI labels to MNI-305 coordinates and was wondering if all issues were resolved but not posted to the list. I attempted the same commands as were recommended in the original conversation: *mri_annotation2labe

Re: [Freesurfer] direction for restart in the middle

Thanks, Bruce. - Don > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer- > boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl > Sent: Wednesday, November 18, 2015 8:55 AM > To: Freesurfer support list > Subject: Re: [Freesurfer] direction for restar

Re: [Freesurfer] Hippocampal Subfields 6.0 with 5.3 recons

Hi Andrew, it's perfectly possible. It would just make your results a bit harder to reproduce, but that's about it ;-) Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer

[Freesurfer] Hippocampal Subfields 6.0 with 5.3 recons

Hello all, I was wondering if anyone with knowledge of the new hippocampal subfield segmentation that is going to be released with version 6.0 could answer a quick question. We have previously processed subjects in v5.3 and would like to use the new hippocampal seg algorithm. How "standalone"

[Freesurfer] Issue with Talairach - mritotal

We are getting an error with recon-all at the stage of Talairach slignment. The error is the one described on the known issues: Can't locate shellwords.pl in @INC. We are running perl5.18, so I downloaded and installed perl5.12 and changed the first line of mritotal as indicated on the ReleaseNo

Re: [Freesurfer] direction for restart in the middle

Hi Don the defect is too big to fix, and probably means something dramatic is wrong (e.g. skull or cerebellum attached to the brain component of the wm.mgz). Check out the ?h.inflated.nofix and see what is going on and correct it before rerunning cheers Bruce On Wed, 18 Nov 2015, Krieger, Do

[Freesurfer] direction for restart in the middle

I have run freesurfer 6Beta on the scan with very large CSF spaces With flags: -bigventricles and -notal-check . I used the latter flag per suggestions in the log as the first run failed on a talaraich check. This second run appears to be hung as it has not written anything new into the recon-all

Re: [Freesurfer] How to edit the corpus callosum segmentation

Hi Geneviève did the mri_cc step work? Looking at the code it (inexplicably) limits the max # of divisions to 5. I'm surprised it didn't segfault. If that part worked I defer to Doug on the rest, but if not we can send you a new mri_cc that should fix the problem cheers Bruce On Wed, 18 Nov

Re: [Freesurfer] -hippocampal-subfields-T1

Hi Daniele, do you think you could send us the subject? norm.mgz, wmparc.mgz and aseg.mgz should be enough. Also, have you experienced this problem with other subjects? Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Av

[Freesurfer] -hippocampal-subfields-T1

dear all, I'm running analysis with the new FS-v6.0 using the flag -hippocampal-subfields-T1 and I get the following error: none Matrix: -3.3 0 0 0 0 -3.3 0 3.3 0 Offset: [-34.0783, 128.423, -71.9905] Center: [0, 0, 0] Translation: [-34.0783, 128.423, -71.9905]