Re: [Freesurfer] Extracting White Matter Structures without using Tracula
Hi Bruce, Our main concern is that we will be incorporating additional sources of error by doing so! But it seems there is no way to get around it. Thanks for the prompt response! Maryam On Tue, May 31, 2016 at 7:07 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > Hi Maryam > > why don't you want to use tracula? That is what it is designed for > > cheers > Bruce > On Tue, > 31 May 2016, Syeda Wajiha Maryam wrote: > > > Hello Freesurfer experts, > > > > I am looking to extract certain white matter pathways (for instance, the > > superior longitudinal fasciculus, uncinate fasciculus) with freesurfer > which > > I believe are affected by Alzheimer's Disease. But it seems that these > can > > only be obtained by performing tractography using Tracula. I was > wondering > > if there was some other way to obtain the labels for these structures > > without having to do so? > > > > Thanks in advance. > > > > Regards, > > Maryam > > > > > ___ > 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 > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ 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 addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Extracting White Matter Structures without using Tracula
Hello Freesurfer experts, I am looking to extract certain white matter pathways (for instance, the superior longitudinal fasciculus, uncinate fasciculus) with freesurfer which I believe are affected by Alzheimer's Disease. But it seems that these can only be obtained by performing tractography using Tracula. I was wondering if there was some other way to obtain the labels for these structures without having to do so? Thanks in advance. Regards, Maryam ___ 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 addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Basal Ganglia Segmentation
I definitely meant to type *Dear in my email. Cheers, Maryam On Thu, Feb 11, 2016 at 2:57 PM, Syeda Wajiha Maryam <s.veggi...@gmail.com> wrote: > Fear Freesurfer Experts, > > I have a feeling this question has been asked already but I'm still > confused about it. Is there a way to extract the basal ganglia structure > using freesurfer? > > Thanks in advance for your help! > > Regards, > Maryam > ___ 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 addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Basal Ganglia Segmentation
Fear Freesurfer Experts, I have a feeling this question has been asked already but I'm still confused about it. Is there a way to extract the basal ganglia structure using freesurfer? Thanks in advance for your help! Regards, Maryam ___ 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 addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Segmentation fault using mri_label2vol
Hello Freesurfer experts, I'm getting a segmentation fault when I use the mri_label2vol command to push aseg labels from freesurfer space to my subject's original T1 space (using the example given on the freesurfer website). I'm not sure why this is happening...I've tried changing the parameters countless times but nothing has worked. I also checked my "aseg.mgz" to make sure it's not corrupted but that isn't the issue either. Any help would be highly appreciated!! Thanks in advance mri_label2vol --regheader /scratch/o/olegm/olegm/2015/test_waj/aseg.mgz --seg /tmp/tmpUj4qzA/aseg2raw/aseg.mgz --temp /scratch/o/olegm/olegm/2015/test_waj/rawavg.mgz --o /tmp/tmpUj4qzA/aseg2raw/aseg_vol.nii.gz Number of labels: 0 Annot File: (null) Template Volume: /scratch/o/olegm/olegm/2015/test_waj/rawavg.mgz Outut Volume: /tmp/tmpUj4qzA/aseg2raw/aseg_vol.nii.gz Registration File: (null) Fill Threshold: 0 Label Vox Vol: 1 ProjType: (null) ProjTypeId: 0 ProjStart: 0 ProjStop: 0 ProjDelta: 0.1 Subject: (null) Hemi: (null) UseNewASeg2Vol: 1 DoLabelStatVol 0 LabelCodeOffset 0 setenv SUBJECTS_DIR /scratch/o/olegm/olegm/subjects $Id: mri_label2vol.c,v 1.34.2.5 2012/06/08 17:31:03 greve Exp $ Template RAS-to-Vox: -0.985 0.000 0.000 128.000; -0.000 -0.000 -0.985 128.000; -0.000 0.833 -0.000 98.000; 0.000 0.000 0.000 1.000; Template Voxel Volume: 1.23773 nHits Thresh: 0 Computing registration based on header RegMat: 1.000 0.000 0.000 -0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; Label RAS-to-Vox: -0.985 0.000 0.000 128.000; 0.000 0.000 -0.985 128.000; 0.000 0.833 0.000 98.000; 0.000 0.000 0.000 1.000; ASeg2Vol: Building LUT Segmentation fault ___ 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 addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
