[Freesurfer] Error using LGI script despite making suggested chages to Matlab script.

Hi, I'm looking to please get some help with -lgi. I'm using matlab R2015b and FS5.3 with recon-all -s subj_id -lgi on os x 10.11. Looking at the output, the first error occurs about here: preparing pial mesh structure ... ...searching for mesh edges...done (206.94 sec). ... creating path

[Freesurfer] Anatomy File Orientation Question

Hi all, Sorry to re-post: I am trying to bring my FreeSurfer brainmask into SPM and then to coregister it (along with some ROIs from FreeSurfer) to the same subject's mprage already processed (coregistered to functional data) in SPM. To do this, I used: mri_convert brainmask.mgz

Re: [Freesurfer] Co-registering different source data

I have tried multiple variations for my subject directory. I have had it end at study11074, S2sdt, segfs, and label. I suspected it should either be S2sdt or segfs. I get the same error in all cases still. When using a differnt function with the subject directory path, I had ended at S2sdt, the

[Freesurfer] Re Re Re Re: Question regarding mri_convert

The differences have been found in the outputs from the aseg file. Particularly, I am interested in the ventricles and the intracranial volumes. I have loaded both anatomicals in FreeView and toggled between them and have found no differences visually. I have attached the files (Via Google Drive

Re: [Freesurfer] Do you suggest to denoise T1 before feed it to Freesurfer

Hi Zhengchen I don't think there is a general answer to your question as it depends on how noisy the input image is, what denoising algorithm you use and what outcome measures you care about. For example, it might improve putamen/pallidum but worsen thickness measures in low contrast regions

Re: [Freesurfer] Co-registering different source data

I think you SUBJECTS_DIR might be set incorrectly, /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label I suspect the value should be: /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/ or possibly something else: ${SUBJECTS_DIR}/$SUBJECT/label/ should be the directory with

[Freesurfer] Do you suggest to denoise T1 before feed it to Freesurfer

Hi Freesurfers, In order to get the better segmentation and surfaces by Freesurfer, do you think it is necessary to denoise T1 before feed it to Freesurfer? Since there are several advanced MRI denoising methods which are not covered in FS preprocessing, I though it would be better to perform one

Re: [Freesurfer] Co-registering different source data

Th output is below: aparc.annot.a2009s.ctab lh.BA45.label lh.V2.thresh.label rh.BA4p.label aparc.annot.ctab lh.BA45.thresh.labelrh.aparc.a2009s.annot rh.BA4p.thresh.label aparc.annot.DKTatlas40.ctab lh.BA4a.label rh.aparc.annot

Re: [Freesurfer] Freeview Loading Volumes

Hi Bob, I think freeview by default automatically locates to the default mri directory under the current subject. It is convenient in some use case but apparently not so much in your case. I will make that optional or figure out a better way to handle this. Best, Ruopeng On 9/25/2016 9:46

Re: [Freesurfer] Co-registering different source data

Thank you. That worked for changing the default directory. When I run mri_label2label, I am still getting the same error that there is no such file or directory for the label. Anna From: freesurfer-boun...@nmr.mgh.harvard.edu

Re: [Freesurfer] Co-registering different source data

what is the output of "ls"? On 9/27/16 11:50 AM, Crawford, Anna wrote: > Thank you. That worked for changing the default directory. When I run > mri_label2label, I am still getting the same error that there is no such file > or directory for the label. > > Anna >

Re: [Freesurfer] Co-registering different source data

Anna, if you are using bash the command is: export SUBJECTS_DIR= On 9/27/16 11:31 AM, Crawford, Anna wrote: > I also tried doing setenv SUBJECTS_DIR but that did not work either. > > bash: setenv: command not found > > Thanks, > Anna > > From: Crawford,

Re: [Freesurfer] Coordinates of particular volumes

I think your first argument to ind2sub needs to be size(mri.vol) cheers Bruce On Tue, 27 Sep 2016, Aziz Nanthaamornphong wrote: I have tried to get the coordinates with following commands: mri = MRIread('aseg.mgz'); pos = find(mri.vol == 17); [i,j,k] = ind2sub(10213,pos); However, I found

Re: [Freesurfer] Co-registering different source data

If I don't use --sd it uses the default subject directory (SUBJECTS_DIR /tools/freesurfer/subjects) which is not where my data is located. Thanks, Anna From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of

Re: [Freesurfer] Coordinates of particular volumes

Aziz, Try this: [i,j,k]=find(mri.vol==17) and get rid of the ind2sub call hth d On Tue, Sep 27, 2016 at 2:00 AM, Aziz Nanthaamornphong wrote: > I have tried to get the coordinates with following commands: > > mri = MRIread('aseg.mgz'); > pos = find(mri.vol == 17); >

Re: [Freesurfer] Co-registering different source data

Do you need to use the ---sd option? That sets the SUBJECTS_DIR. If that is already set properly, then do not use the --sd. On 9/27/16 9:38 AM, Crawford, Anna wrote: > Hi, > > I keep getting an error when I use mri_label2label. Below is my input and > output. I have tried various paths all the

Re: [Freesurfer] Coordinates of particular volumes (fwd)

the command should be [i,j,k] = ind2sub(mri.volsize,pos); -- Forwarded message -- Date: Tue, 27 Sep 2016 13:00:51 +0700 From: Aziz Nanthaamornphong Reply-To: Freesurfer support list To: Freesurfer support list

[Freesurfer] optseq help

Dear all, I would like to optimize my design by inserting null-events between my trials (in order to better catch the HRF shape with reasonable duration of the experiment) using optseq. I'm not very familiar with this useful tool and I wonder if you could check my setup? Here my design : I've

Re: [Freesurfer] Co-registering different source data

Hi, I keep getting an error when I use mri_label2label. Below is my input and output. I have tried various paths all the way down to the label and above the subject level, but still always get the same error. I have also verified it is the path with the label. Why is it not recognizing it?

[Freesurfer] QDEC error writing fsgd and generating contrasts

Dear FreeSurfer Developers, I have the following problem and would be very happy if you could help me. I have searched the list and did not find the solution to my problem. I am using FS 5.1 because I have to reanalyze data which I preprocessed in 2014. Back then recon-all and all the

[Freesurfer] QDEC error writing fsgd and generating contrasts

Dear FreeSurfer Developers, I have the following problem and would be very happy if you could help me. I have searched the list and did not find the solution to my problem. I am using FS 5.1 because I have to reanalyze data which I preprocessed in 2014. Back then recon-all and all the

[Freesurfer] TR: volume to surface for ROI already in orig space

De : Alain Imaging Envoyé : lundi 26 septembre 2016 17:17 À : freesurfer@nmr.mgh.harvard.edu Objet : volume to surface for ROI already in orig space Hi everyone, I've used a couple of ROIs that have been drawn in the mni space for

Re: [Freesurfer] Coordinates of particular volumes

I have tried to get the coordinates with following commands: *mri = MRIread('aseg.mgz');pos = find(mri.vol == 17);* *[i,j,k] = ind2sub(10213,pos);* However, I found that all values of 'j' are 1. is there something wrongs with my strategy? Best Regards, Aziz. On Mon, Sep 12, 2016 at 8:40 PM,