[Freesurfer] Question about talairach.m3z file

. However, I wanted to confirm *which* MNI talairach.m3z represents - it's MNI305, correct? Thanks! Paul -- Paul Beach DO/PhD candidate - Year VI Michigan State University - College of Osteopathic Medicine - Neuroscience Program - Bozoki Lab: Neurology/Radi

[Freesurfer] Fwd: Question about talairach.m3z file

-- Forwarded message -- From: Paul Beach Date: Fri, Sep 27, 2013 at 2:39 PM Subject: Re: [Freesurfer] Question about talairach.m3z file To: Bruce Fischl So would you suggest, then, that it would be better to use the mri_vol2vol command to transform subject data (anatomical and

[Freesurfer] MNI152 to 305 conversion

tput.mni305.2mm.nii.gz* *>>* *>> This will resample MNI152_T1_2mm.nii.gz (or anything in that space) to the* *>> mni305 2mm space.* However, this changing the orientation of my data - essentially all images are being rotated 90degrees so the frontal lobe is pointed straight up. Are ther

[Freesurfer] running recon-all for FSL-based ROIs

[L] -step- 2.000 mm [ 91 voxels] A-to-P extent: -90.000 [A] -to- 126.000 [P] -step- 2.000 mm [109 voxels] I-to-S extent: -72.000 [I] -to- 108.000 [S] -step- 2.000 mm [ 91 voxels] Thanks! -- Paul Beach DO/PhD candidate - Year VI Michigan State University - College of Osteopa

[Freesurfer] mri_surf2surf error - 'could not determine type of...'

rig.mgz --identity* Any suggestions for getting past this error? Thanks for your help, Paul -- Paul Beach DO/PhD candidate - Year VI Michigan State University - College of Osteopathic Medicine - Neuroscience Program - Bozoki Lab: Neurology/Radiology ___

Re: [Freesurfer] mri_surf2surf error - 'could not determine type of...'

ouglas N Greve wrote: > > The full error msg is not in the subject line. My guess is that the > "lh." in front of "Yeo" in the srcsurfval is causing the problem > > > On 10/23/2013 03:17 PM, Paul Beach wrote: > > Hello FS experts, > > > > I&#

Re: [Freesurfer] mri_surf2surf error - 'could not determine type of...'

That worked like a charm. Thanks! On Wed, Oct 23, 2013 at 5:14 PM, Bruce Fischl wrote: > try specifying --sval-annot Yeo2011_17Networks_N1000.annot instead of > --srcsurfval > > cheers > Bruce > > On Wed, 23 Oct 2013, Paul Beach wrote: > > Apologies: the full er

[Freesurfer] converting to fsaverage space

oving things in fsaverage space to individual subject space. Unfortunately, when I try to load the above output file into tkmedit for fsaverage as an aux volume it's essentially off screen (i.e. not in the brain). Obviously the output file is not in fsaverage space, per se. Any thoughts on h

[Freesurfer] Fwd: converting to fsaverage space

oving things in fsaverage space to individual subject space. Unfortunately, when I try to load the above output file into tkmedit for fsaverage as an aux volume it's essentially off screen (i.e. not in the brain). Obviously the output file is not in fsaverage space, per se. Any thoughts on h

Re: [Freesurfer] Fwd: converting to fsaverage space

> doug > > > > On 11/27/13 2:57 PM, Paul Beach wrote: > > Freesurfer experts, > > I am interested in converting functional ROIs defined by the Greicius > lab (http://findlab.stanford.edu/functional_ROIs.html) into individual > subject space. Originally I had conv

Re: [Freesurfer] Desikan-Killiany parcellations of SI+SII and IPL

or 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 > dispo

Re: [Freesurfer] hypothalamus?

Ella, My understanding is the same. I've made my own ROI by hand drawing on the average subject and using various commands to map onto individual subjects. If you're doing resting analysis then you can check your general whole brain correlation results against the literature to see if your ROI

Re: [Freesurfer] Convert processed RS time series to MNI152

the anatomical (bbregister), then use mri_vol2vol with the > --fstal option > > On 05/08/2014 04:31 PM, Paul Beach wrote: > >> Hi Freesurfers, > >> > >> I have several processed resting time series files (processed through > >> AFNI) and I'd like to c

[Freesurfer] mapping extracted MNI152 ROIs to individual subjects

mmand that would guide me in developing the line of code to write. Thanks! -- Paul Beach DO/PhD candidate - Year VI Michigan State University - College of Osteopathic Medicine - Neuroscience Program - Bozoki Lab: Neurology/Radiology ___ Freesur

[Freesurfer] separate FSAverages and surface-based ROIs

my case, subject groups separated by disease state)? and Does anyone have any advice on how to get hand-drawn surface-based ROIs from Freesurfer's tksurfer into AFNI that full cover the entirety of the gray matter? Cheers and thanks! -- Paul Beach ___

[Freesurfer] extracting hand drawn ROIs to Afni space

Hi there, Through the help of the Freesurfer Q&A staff I've been able to get ROIs drawn in tksurfer into an augmented aparc+aseg file of an averaged subject. I need to be able to get those ROIs, which are not part of the color LUT, into Afni space. For ROIs that are already in the LUT, getting th

Re: [Freesurfer] extracting hand drawn ROIs to Afni space

r help! Paul On Mon, Feb 18, 2013 at 3:13 PM, Bruce Fischl wrote: > Hi Paul > > we usually call those labels and have an ascii label file format. Not sure > how to get that into AFNI, but I'm zure Ziad (ccd) knows. > > cheers > Bruce > > On Mon, 18 Feb 2013, Paul Be

Re: [Freesurfer] extracting hand drawn ROIs to Afni space

l > > I don't know how well you know how to use the SUMA tools I mentioned > above, but if you need more detailed help let me know. > > cheers, > Ziad > > On Feb 18, 2013, at 4:39 PM, Paul Beach wrote: > > Thank you for forwarding this. > > I realize I nee

Re: [Freesurfer] bbregister to register a .annot file to MNI space

tinfo/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 >

[Freesurfer] CTABreadASCII error with mris_label2annot

rn/research/PI/training/beachpau/Beach_FreeSurfer_data/HS_001/label/rh.Yeo_7Net_split_aparc.annot* I have attached my .ctab files in case they would help. -- Paul Beach DO/PhD candidate - Year VI Michigan State University - College of Osteopathic Medicine - Neuroscience Program

Re: [Freesurfer] CTABreadASCII error with mris_label2annot

Oy. Thanks - that worked. On Wed, May 21, 2014 at 11:21 AM, Douglas N Greve wrote: > Your color table appears to have been created in windows (or maybe mac). > Convert it to a unix text file. > doug > > > On 05/21/2014 10:40 AM, Paul Beach wrote: > > Freesurfer folk

Re: [Freesurfer] ?reference(s) supporting DLPFC label

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. > > -- Paul Beach DO/PhD candidate - Year VI Michigan State University - College of Osteopathic Medicine - Neuroscience Prog

Re: [Freesurfer] Freesurfer Surface based ROI to AFNI?

t > 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. > > -- Paul Beach DO/PhD candidate - Year VI Michigan

Re: [Freesurfer] Freesurfer Surface based ROI to AFNI?

next step I > am running into issues. > > I don't seem to see any medial wall in the aparc annotation. Plus I am not > familiar with the color table, I was just wondering what that would look > like. > > Any help from anyone would be much appreciated! > > Tara >

[Freesurfer] Improving translation of Choi striatal ROIs to original domain

uld be to do a recon-all based procedure, but I have no clue what commands within the recon-all domain that would involve. Thanks for your suggestions. -- Paul Beach DO/PhD candidate - Year VI Michigan State University - College of Osteopathic Medicine - Neuroscience Program - MSU *Co*gnitiv

[Freesurfer] Fwd: Improving translation of Choi striatal ROIs to original domain

uld be to do a recon-all based procedure, but I have no clue what commands within the recon-all domain that would involve. Thanks for your suggestions. -- Paul Beach DO/PhD candidate - Year VI Michigan State University - College of Osteopathic Medicine - Neuroscience Program - MSU *Co*gnitiv

Re: [Freesurfer] Fwd: Improving translation of Choi striatal ROIs to original domain

ading email for a while > > cheers > Bruce > > > > On Wed, 18 Jun 2014, Paul Beach wrote: > > Hi Freesurfers, >> My processing stream involves moving the parcellated functional networks >> of >> Yeo and Choi to original subject domain to do connecti

Re: [Freesurfer] Fwd: Improving translation of Choi striatal ROIs to original domain

king a set of >> ROIs/parcellations defined in some (non-probabilistic) atlas and warping >> them to each subject via an affine transformation, which is what it sounds >> like you are doing with the "Choi ROIs". >> >> cheers, >> -MH >> >> -- >> Michael Harms, Ph.D. >> ---

Re: [Freesurfer] insula on medial surface

___ > 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

Re: [Freesurfer] fsaverage subject does not exist in SUBJECTS_DIR

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 Complian

Re: [Freesurfer] fsaverage subject does not exist in SUBJECTS_DIR

o does it mean that the > program couldn't make a link between my actual image places and > $FREESURFER_HOME/subjects/fsaverage > ? > what can I do to fix it ? > > Thank you, > Mahmoud > > On Wed, Sep 17, 2014 at 9:16 AM, Paul Beach wrote: > >> The g

Re: [Freesurfer] fsaverage subject does not exist in SUBJECTS_DIR

aul, > > I tried this: > SUBJECTS_DIR=/mnt/hgfs/DBSI/volumetric/MGZ > cd $SUBJECTS_DIR > ln -s $FREESURFER_HOME/subjects/fsaverage > > and got this: > ln: failed to create symbolic link ‘./fsaverage’: Operation not supported > > any idea ? > > Mahmoud > >

Re: [Freesurfer] fsaverage subject does not exist in SUBJECTS_DIR

Hmm. Well I'm stumped. Sorry. :-/ Any Freesurfer gurus have some ideas here? On Wed, Sep 17, 2014 at 9:59 AM, Mahmoud wrote: > Paul > > it shows again: > ln: failed to create symbolic link ‘./fsaverage’: Operation not supported > > !!! > > On Wed, Sep 17, 2014

Re: [Freesurfer] fsaverage subject does not exist in SUBJECTS_DIR

Yeah, I was starting to wonder if he was having permissions issues as well. On Wed, Sep 17, 2014 at 10:16 AM, Mahmoud wrote: > Paul, > > I am using bash instead of tcsh. Does it make any difference ? > > Mahmoud > > On Wed, Sep 17, 2014 at 7:09 AM, Paul Beach wrote: >