Re: [Freesurfer] volumes per lobe

> > cd $SUBJECTS_DIR/subject/scripts > mri_annotation2label --subject vol17 --hemi rh --lobesStrict lh.lobesfile > mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f > ../stats/lh.lobesfile.stats -b -a ../label/lh.lobesfile.annot subject > lh white > > doug &g

[Freesurfer] volumes per lobe

ified mean curvature = 0.149 average integrated rectified Gaussian curvature = 0.106 folding index = 4797 intrinsic curvature index = 391.1 Can somebody guide me? Thank you in advance, -- -- *Carolina Valencia * The information contained in this me

[Freesurfer] ERROR: You are trying to re-run an existing subject

en omit all -i flags. -- -- *Carolina Valencia Muñoz* ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is ad

[Freesurfer] errors Quantifying Hippocampal Subfield Segmentations

mgz \ > -p-labels posterior_left_* posterior_Left-Hippocampus.mgz \ > -p-labels posterior_right_* posterior_Right-Hippocampus.mgz \ > -p-prefix posterior_ -p-lut $FREESURFER_HOME/FreeSurferColorLUT.txt freeview.bin: No match. Am I miss something?

[Freesurfer] hippocampal subfield segmentation

Hi Freesurfer community, A quick question, how long takes to run the hippocampal subfield segmentation for a subject that has already run the typical recon-all pipeline? Thank you, -- -- *Carolina Valencia M * ___ Freesurfer mailing list Freesurfer

[Freesurfer] TRACULA exited with errors

ess my own data. I have to recon-all my structural data and to have the orig DWI dicoms in order to use trac-all, right? Many thanks, Best regards -- -- *Carolina Valencia M* ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard

[Freesurfer] Multiple sclerosis lesions

Dear FS users, I would like to use FS to calculate WM hypointensitis (so-called black holes) for patients with multiple sclerosis, but 1. I don't know which stat file I should use to report the volumes, such as total WM, WM hypointensities, etc 2. which editing tool I must use when the lesion is no

Re: [Freesurfer] tkmedit bus error

C_vol01 rh pial > > Sincerely, > > > Gonzalo Rojas Costa > Department of Radiology > Clinica Las Condes > Santiago > Chile > > > > Message: 4 > > Date: Sun, 18 Sep 2011 10:25:26 -0400 (EDT) > > From: Bruce Fischl > > Subject: Re: [Freesurfer] tkme

[Freesurfer] tkmedit bus error

Hi FSusers I run recon-all in a patient without problems, but when I tried to view it in tkmedit, an error pops up. I appreciate your help! Best regards, Carolina recon-all -s CORBIC_vol01 finished without error at Tue Sep 13 12:42:43 COT 2011 done cvalencia-Precision-WorkStation-T3400:~> tkmed

[Freesurfer] dcm2nii and recon all

Dear FS' users, I have a 3D T1 from a GE scanner which I convert with dcm2nii to use it with recon-all, but I got 3 images: o -- original oo -- orthogonal co -- cropped image Which I should use to run the command recon-all? thanks! Carolina ___ Freesu

Re: [Freesurfer] update v5.1 and trac-all command

> Hm, it seems like all FSL commands give you a shared library error. Were > you able to run FSL commands properly before updating freesusrfer? > > On Thu, 18 Aug 2011, Carolina Valencia wrote: > > Hi,After update the FS version to 5.1, I follow the Tracula tutorial and >> r

Re: [Freesurfer] update v5.1 and trac-all command

any suggestions?? Thanks, Carolina 2011/8/16 Anastasia Yendiki > > Hi Carolina - There's info on the new release and how to install it here: > https://surfer.nmr.mgh.**harvard.edu/fswiki/**ReleaseNotes<https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes> > > a.y > &

[Freesurfer] update v5.1 and trac-all command

Hi FS'users, I'm trying to do the Tracula tutorial but after set the configuration file I run the command trac-all cvalencia-Precision-WorkStation-T3400:~/freesurfer/subjects/Tracula_Tutorial_Public/diffusion_tutorial> trac-all -help trac-all: Command not found. I have the version: freesurfer-Linu

Re: [Freesurfer] Cortical segmentation error

n't recommend it). The surfaces are. As for the heterotopias, I don't > really know what a good output would be. It depends what you want to do with > them. I guess they should be gray matter, no? > > Bruce > > > > On Thu, 21 Jul 2011, Carolina Valencia wrote: &g

Re: [Freesurfer] Cortical segmentation error

on't look at the colored overlay - that is the aseg voxel > segmentation and not what we typically use for cortical morphometry. Only > look at the yellow and red lines. > > > cheers > Bruce > On Tue, 19 Jul 2011, Carolina Valencia wrote: > > tiff I guess, I too

[Freesurfer] Cortical segmentation error

Dear FS experts, I'm trying to analyse a case of cortical dysplasia, but after recon-all I see some errors in tkmedit that I don't know what to edit. I found some errors in cortical and subcortical segmentation, I don't find in the failure mode presentation a way to solve this. I saw the pial surf

Re: [Freesurfer] cortical dysplasia

Hi Pedro, I tried to send you the image of my problem but the mailing list rejected my attachment, despite the file is only 769 k. How I can post an image in order to illustrate my problem? Thanks, Carolina 2011/7/7 Carolina Valencia > Hi Pedro, > > Yes I have a case with heterotop

[Freesurfer] talaraich ERROR

Hi FSexperts, I have a case of a child with *Hydrocephalus and cortical dysplasia, the patient has a subcutaneous ventriculo-peritoneal shunt that produces an artifice in all MRI sequences, I try to recon-all but it exit with ERROR* # #@# Talairach Failu

[Freesurfer] cortical dysplasia

Hello FSexperts I have a MPRAGE image of cortical dysplasia, I have some regions of grey matter within the white matter, and I measured the cortical thickness in the projections of those regions and I expected to find a thinnercortex instead I found a cortical thickening. FS takes into account the

Re: [Freesurfer] Matlab and FS

> can try with Octave (a kind of GNU Matlab for Linux). > > ** ** > > Cheers **** > > Jorge > > --- El *mar, 5/7/11, Carolina Valencia *escribió: > > > De: Carolina Valencia > Asunto: [Freesurfer] Matlab and FS > Para: freesurfer@nmr.mgh.harvard.edu &

[Freesurfer] Matlab and FS

Hello FS'users, I'm trying to do an histogram of cortical thickness for 2 cases in matlab, but the problem is that I have Installed matlab in a computer (windows) and FS in another one (ubuntu) Can I configure something to use the FS commands in matlab in order to obtain some graphs? And also, whe

Re: [Freesurfer] recon-all -s exited with ERRORS

Thanks a lot, it works. just waiting 24 hours. Best regards, Carolina 2011/6/10 > Hi Carolina, > > Sorry My bad. I was inaccurate in my previous message. > > -subject should work. > > Assuming that the MPRAGE of your subject is under the following directory: > > /freesurfer/subjects/buckner_da

[Freesurfer] recon-all -s exited with ERRORS

Hello Freesurfer's users, I'm starting using FS and I have a problem running recon-all I create a folder called hptu_subj001 which contains MPRAGE.nii.gz within tutorial_subj First I convert nii.gz to mgz qith the command: recon-all -i MPRAGE.nii.gz -s hptu_subj001 and then in order to process all

[Freesurfer] GUI analysis

Dear freesurfer users I want to know where I can find the GUI that assist in the management and analysis of groups of data not shown in the FreeSurfer Analysis Pipeline Overview Thanks, Carolina ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.ed

Re: [Freesurfer] installation problem in ubuntu

t; -- PPJ > > Please: cc the freesurfer list when answering > > 2011/2/22 Carolina Valencia > > Hi Pedro, >> >> Finally, I could install it with the license file and the environment is >> properly set without warnings. >> But trying to test it,

Re: [Freesurfer] installation problem in ubuntu

Hi Bruce, I'm experimenting problems with the installation on Ubuntu too. There's is warning in the welcome message, it seems that something is missing: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) WARNING: /home/cvale

[Freesurfer] testing FreeSurfer

Hi FreeSurfer's user, I'm new using this software, I try to install on Ubuntu and to set up following the recommendation of the webpage. Then I tried to test but any commmand seems to be recognized, also when I started a new terminal a warning is shown: freesurfer-Linux-centos4_x86_64-st

[Freesurfer] testing FreeSurfer

Hi FreeSurfer's user, I'm new using this software, I try to install on Ubuntu and to set up following the recommendation of the webpage. Then I tried to test but any commmand seems to be recognized, also when I started a new terminal a warning is shown: freesurfer-Linux-centos4_x86_64-sta