[Freesurfer] Parcellated regions as masks?

Hi FS users, We've T1 and EPI images collected. For my analysis I want to use FS parcellated regions (both cortical/sub-cortical regions) as ROIs (Masks) for my functional images. Would anyone kindly let me know what is the best way to proceed. Cheers, Sabin Khadka

Re: [Freesurfer] Parcellated regions as masks?

Hi Doug- Thanks for the reply. Would you mind elaborating on how exactly to use mri_label2vol to map the aparc+aseg.mgz into the function space ( I could not find the correct syntax that should be used)? Also, what should i do if I want individual masks for each ROI?  Cheers, Sabin Khadka

[Freesurfer] Extract mean time series from parcellated region

Hi FS user, I am trying to extract time series of fmri rest data of certain parcellated regions (both cortical and subcortical). for that I am doing following # bbregister --s --mov --init-fsl --reg register.dat --bold# mri_label2vol --aparc+aseg --subject --temp --fillthresh 0.5 --reg regs

Re: [Freesurfer] Extract mean time series from parcellated region

Hi Doug- The command doesn't error out but it just give me one value. I was assuming the following command would give me value in  time series x mean value in text file. Am I following correct strategy/commands? Cheers, Sabin Khadka From: Douglas Greve To: sabin khadka ; Frees

Re: [Freesurfer] Extract mean time series from parcellated region

.nii.gzEPI.nii.gz is 4D image with 210 frames. How can I get test1.nii.gz and test2.nii.gz in 4D format? Should be something basic but I could not figure out how. I appreciate your help!!  Cheers, Sabin Khadka From: Douglas Greve To: sabin khadka ; Freesurfer support list Sent: Tuesday

Re: [Freesurfer] Extract mean time series from parcellated region

Works fine. thanks for the help Doug. Cheers, Sabin Khadka From: Douglas Greve To: sabin khadka ; Freesurfer support list Sent: Tuesday, January 27, 2015 12:33 PM Subject: Re: [Freesurfer] Extract mean time series from parcellated region That label2vol command maps the aseg

[Freesurfer] time series data from FSFAST

Hi FS Users, I've preprocessed resting state fmri data using preproc-sess as shown in FSFAST functional connectivity walk through manual. I know I can extract mean time series of a seed region using fcseed-sess. I am trying to find a command to extract mean time series from all Desikan (or Dest

Re: [Freesurfer] time series data from FSFAST

doingmri_segstats --seg fsaverage/mri/aseg.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --avgwf test2.txtbut it gave me dimension mismatch error. I'd appreciate if you'd direct me on how to get average time series values from subcortical regions.  Cheers, Sabin Khadka From: Douglas

Re: [Freesurfer] time series data from FSFAST

Hi Doug- Works fine. I appreciate your help. Related but different question: Would you help me understand how the QA value(0-1)while checking registration using following command is calculated. tkregister-sess -s sess01 -s sess02 -s sess03 -fsd bold -per-run -bbr-sum  Cheers, Sabin Khadka

[Freesurfer] FSFAST

Hi FS Users- After using FSFAST's preproc-sess command (I get the output files: fmcpr.up.sm5.fsaverage.lh.nii.gz,fmcpr.up.sm5.fsaverage.rh.nii.gz, fmcpr.up.sm5.mni305.nii.gz), I was wondering if we could see or tell how well the EPIs are mapping onto the common space (I am assuming fsaverage in

[Freesurfer] FS-FAST bbr registration

Hi all- Is there a command we can have screenshots (similar to one employed in fsl) of fucntional--> structural registration in FSFAST to visually check the registration on top of the BBR cost?   Cheers, Sabin Khadka ___ Freesurfer mailing l

[Freesurfer] FSFAST

Hi all,If I understand correctly, preproc-sess command takes mid point of EPI image as reference and make template and calculate motion parameters. I could not figure if I could use different image as reference, is it possible? Cheers, Sabin Khadka___

[Freesurfer] FSFAST- Cerebellum

Hi all, I am trying to extract mean time series BOLD data using FSFAST from Cortical ROIs + sub cortical ROIs and cerebellum. preproc-sess -s rest210 -fsd bold -surface fsaverage lhrh -mni305 -fwhm 6 -per-run -stc odd    mri_segstats --annot fsaverage lh aparc --i rest210/bold/001/fmcpr.odd.sm6.

[Freesurfer] FSFAST- Cerebellum

exactly to extract time series from cerebellar regions. So if I want to extract time series from regions as described in Buckner et.al 2011. Could I just use mri_segstats for the labels 601-628 in FreeSurferCololLUT.txt? If not could you please direct me to processes that I can use. Cheers, Sabin

Re: [Freesurfer] FSFAST- Cerebellum

if I have to use some other scripts commands (other than mri_segstats). Cheers, Sabin Khadka On Mon, Jun 20, 2016 at 10:20 PM, Thomas Yeo wrote: > Hi Sabin, > > The structures 601-628 FreeSurferCololLUT.txt correspond to anatomical > substructures of the cerebellum (e.g., Crus I, e

Re: [Freesurfer] FSFAST- Cerebellum

doing anything wrong here. Do you have any suggestions/fixes? Cheers, Sabin Khadka On Fri, Jun 24, 2016 at 6:30 AM, Thomas Yeo wrote: > Hi Doug, thanks. > > Hi Sabin, you can use the following steps to transform the Buckner > cerebellum atlas to your subject's native anatomic

Re: [Freesurfer] FSFAST- Cerebellum

Hi Thomas- On second thought is it valid to simply do if I want average time series of the cerebellum regions? fslmeants -i fmcpr.anat.nii.gz -m Buckner_atlas_FSSub.nii.gz >> avgCerebellum.txt Is this correct? Cheers, Sabin Khadka On Mon, Jun 27, 2016 at 11:36 AM, Sabin Khadka wrote:

Re: [Freesurfer] FSFAST time series extraction

_FSSub_m47.nii.gz --ctab $FREESURFER_HOME/average/Yeo_JNeurophysiol11_MNI152/Yeo2011_7Networks_ColorLUT.txt --excludeid 0 --i fmcpr.anat.nii.gz --avgwf Cerebellum_networks_R.txt # extract right Cerebellum time series Cheers, Sabin Khadka On Tue, Jul 5, 2016 at 3:48 PM, Douglas N Greve wrote:

[Freesurfer] MNI coordinates of all the vertices of fsaverage

Hi Doug, I tried to pick up from the thread below to get MNI coordinates of each destrieux parcellation region. https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-July/032037.html I created label files from mri_annotation2label --subject fsaverage --hemi lh(/rh) --annotation aparc.a2009

Re: [Freesurfer] MNI coordinates of all the vertices of fsaverage

Anyone? Cheers, Sabin Khadka On Fri, Jul 29, 2016 at 2:47 PM, Sabin Khadka wrote: > Hi Doug, I tried to pick up from the thread below to get MNI coordinates > of each destrieux parcellation region. > > > > https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-July

[Freesurfer] FSFAST ROI atlas

could you please advise me on how do it (if they are at all possible). Cheers, Sabin Khadka ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intende

Re: [Freesurfer] FSFAST ROI atlas

Hi Doug- Do you think it is possible to use these atlas? If so could you point me to steps that needed to be done. Thanks for your help! Cheers, Sabin Khadka On Mon, Aug 15, 2016 at 10:39 AM, Douglas Greve wrote: > I have not used them myself. > > On 8/15/16 10:23 AM, Sabin Kha

Re: [Freesurfer] FSFAST ROI atlas

Hi Michael- Is there anyway I can get those Gordon parcellation annot files? Cheers, Sabin Khadka On Wed, Aug 17, 2016 at 10:59 AM, Harms, Michael wrote: > > FYI: I supplied a version of the “Gordon” parcellation in .annot format to > Bruce a while back. He had expressed an in

Re: [Freesurfer] FSFAST ROI atlas

Hi Michael- Thanks very much for the file. Is there published paper or other documents that I could use as reference for these annotation? Cheers, Sabin Khadka On Wed, Aug 17, 2016 at 12:53 PM, Harms, Michael wrote: > > They are attached (assuming that the FS list allows small attac

[Freesurfer] convert FSFAST files to gifti format

Hi all, Is there a way to convert FSFAST files (fmcpr.odd.sm5.fsaverage.?h.nii.gz) files to convert into gifti format? I've tried mris_convert but it does not work. Thanks for help. Cheers, Sabin Khadka ___ Freesurfer mailing list Frees

Re: [Freesurfer] convert FSFAST files to gifti format

Hi Doug- I did try mris_convert -o $SUBJECTS_DIR/FSsub/surf/lh.white $SUBJECTS_DIR/sub/REST/bold/001/fmcpr.odd.sm5.fsaverage.lh.nii.gz fmcpr.lh.gifit-file.gii I still get freadFloat: frear failed error. Cheers, Sabin Khadka On Tue, Sep 13, 2016 at 2:53 PM, Douglas N Greve wrote: > what

Re: [Freesurfer] convert FSFAST files to gifti format

.fsaverage.?h.nii.gz and fmcpr.odd.sm5.mni305.2mm.nii.gz) into CIFTI format? -Sabin On Tue, Sep 13, 2016 at 3:09 PM Sabin Khadka wrote: > Hi Doug- I did try > mris_convert -o $SUBJECTS_DIR/FSsub/surf/lh.white > $SUBJECTS_DIR/sub/REST/bold/001/fmcpr.odd.sm5.fsaverage.lh.nii.gz > fmcpr.lh.gi

[Freesurfer] Tutorial for linear mixed model toolbox

Hi all, I was just wondering if there is a tutorial or example on how to use linear mixed effect model toolbox for longitudinal analysis. I already processed my structural images with longitudinal processing pipeline from freesurfer. I want to do group analysis where I have 4 groups with N~20-3

[Freesurfer] fReadQdec question

Hi all, I am trying to run fReadQdec.m. My qdec.table.dat file is a tab delimited file. However when it reads to Qdec variable it reads it as N(# of subjects)X1 cell (discounting for all tabs and spaces). I tried debugging the code but it seems to me like it is just a simple read file in matlab.

Re: [Freesurfer] fReadQdec question

each variable that I put in table). -Sabin On Tuesday, February 18, 2014 1:26 PM, Douglas N Greve wrote: yes, it has a certain format. Look at the examples on the wiki doug On 02/18/2014 11:19 AM, sabin khadka wrote: > Hi all, > I am trying to run fReadQdec.m. My qdec.table.dat f

Re: [Freesurfer] fReadQdec question

from? I don't see it in our distribution. On 02/18/2014 03:29 PM, sabin khadka wrote: > Hi Doug, > Thanks for  the reply. Yeah I have my qdec.table.dat file in the same > format as wiki says and in tab delimited format. But when I try to run > fReadQdec it reads it as N(# of

[Freesurfer] No labels file in label directory?

Hi all, I ran recon-all -all and all the subjects finished without any error. However in few subjects directory, labels sub-directory only have lh.cortex.label and rh.cortex.label and not other label files like *.label and *.annot. Could anyone help me on how to fix this. -Sabin

[Freesurfer] asegstats2table error

Hi all, While using asegstats2table, I got following error for few subjects, WARN SUBID: nmeasure 66, expecting 55 It let me extract cortical thickness and surface area using aparcstats2table though. Any suggestions? -SABIN___ Freesurfer mailing list Fr

Re: [Freesurfer] asegstats2table error

aseg.stats file to see which segs are missing. doug On 3/2/14 9:46 AM, sabin khadka wrote: Hi all, >While using asegstats2table, I got following error for few subjects, >WARN SUBID: nmeasure 66, expecting 55 >It let me extract cortical thickness and surface area using aparcstats2table >

[Freesurfer] Vertexwise surface area value?

Hi all, I am trying to extract vertexwise surface area values in an ascii files. For that I am doing mri_surf2surf --hemi ?h --srcsubject area --src_type curv --trgsubject fsaverage --trgsurfval XYZ-area --trg_type curv mris_convert -c XYZ-area ?h.white XYZ-area.asc However I am getting surf

[Freesurfer] Vertex wise surface area values?

Hi all, I am trying to extract vertexwise surface area values in an ascii files. For that I am doing mri_surf2surf --hemi ?h --srcsubject area --src_type curv --trgsubject fsaverage --trgsurfval XYZ-area --trg_type curv mris_convert -c XYZ-area ?h.white XYZ-area.asc However I am getting surfa

[Freesurfer] vertex wise surface area values?

Hi all, I am trying to extract vertexwise surface area values in an ascii files. For that I am doing mri_surf2surf --hemi ?h --srcsubject area --src_type curv --trgsubject fsaverage --trgsurfval XYZ-area --trg_type curv mris_convert -c XYZ-area ?h.white XYZ-area.asc However I am getting surf

[Freesurfer] test- please disregard

- ___ 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

[Freesurfer] test- please disregard

Sorry all. Just a test 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

[Freesurfer] vertex-wise surface area values?

Hi all, I am trying to extract vertexwise surface area values in an ascii files. For that I am doing mri_surf2surf --hemi ?h --srcsubject area --src_type curv --trgsubject fsaverage --trgsurfval XYZ-area --trg_type curv mris_convert -c XYZ-area ?h.white XYZ-area.asc However I am getting surf

[Freesurfer] vertex wise surface area measure?

Hi all, I am trying to extract vertexwise surface area values in an ascii files. For that I am doing mri_surf2surf --hemi ?h --srcsubject area --src_type curv --trgsubject fsaverage --trgsurfval XYZ-area --trg_type curv mris_convert -c XYZ-area ?h.white XYZ-area.asc However I am getting surf

Re: [Freesurfer] Thickness values to a common space

Hi all, Related question to this. I am trying to extract vertexwise surface area values in an ascii files. For that I am doing mri_surf2surf --hemi ?h --srcsubject area --src_type curv --trgsubject fsaverage --trgsurfval XYZ-area --trg_type curv mris_convert -c XYZ-area ?h.white XYZ-area.asc

Re: [Freesurfer] Thickness values to a common space

? Thanks, Sabin On Tuesday, April 15, 2014 11:29 AM, Douglas N Greve wrote: what is your command line? The one below is not a valid command line. On 04/15/2014 11:23 AM, sabin khadka wrote: > Hi all, > > Related question to this. > I am trying to extract vertexwise surface area

[Freesurfer] Extract vertex-wise cortical thickness, surface area and lgi values in ascii files?

Hi all, I want to extract to extract thickness, area and lgi values vertex wise in ascii files for group of subjects. Could anyone suggest me on how to do it. Thank you for your help. -Sabin___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard

Re: [Freesurfer] Extract vertex-wise cortical thickness, surface area and lgi values in ascii files?

ascii file in the format cheers Bruce On Thu, 17 Apr 2014, sabin khadka wrote: > Hi all, > I want to extract to extract thickness, area and lgi values vertex wise in > ascii files for group of subjects. Could anyone suggest me on how to do it. > > Thank you for your hel

Re: [Freesurfer] Extract vertex-wise cortical thickness, surface area and lgi values in ascii files?

, sabin khadka wrote: Ahh. Great. Thanks you very much for the information. I ran mri_surf2surf and then mris_convert to get thickness and surface area vertex wise values. I found that some vertices had negative values of surface area for few subjects. Should not surface area values be positive

[Freesurfer] 2x3 ANOVA question

Hi all, I am trying to run 2x3 factorial model correcting for age, sex and intracranial volume. Just to give you insight in my data I have my fsgd file as GroupDescriptorFile 1 Title DOSS analysis 2x3 factorial Class MaleGroup1Low Class MaleGroup1Medium Class MaleGroup1High Class MaleGroup2Low

[Freesurfer] Qdec - cluster labels

Hi all - When you get a significant cluster after doing monte-carlo simulation, we get peak vertex/Talairach coordinates and also saved in *summary files. Is there a way to find all the parcellated regions (Desikan, or, Destriuex) in the significant clusters? Thanks,Sabin ___

[Freesurfer] Qdec questions

Hi all - When you get a significant cluster after doing monte-carlo simulation, we get peak vertex/Talairach coordinates and also saved in *summary files. Is there a way to find all the parcellated regions (Desikan, or, Destriuex) in the significant clusters? Thanks

[Freesurfer] Qdec question

Hi all - When you get a significant cluster after doing monte-carlo simulation, we get peak vertex/Talairach coordinates and also saved in *summary files. Is there a way to find all the parcellated regions (Desikan, or, Destriuex) in the significant clusters? Thanks_

[Freesurfer] Significant clusters from mri_glmfit

Hi all, I used FDR correction method to correct for multiple comparison after mri_glmfit. And I have a cluster covering multiple regions. I want to extract the thickness, surface area, lgi values for local maxima (or, multiple regions covered by the big significant cluster). I see it is not stra

[Freesurfer] extract mean thickness, surface area of ROI

Hi all, I want to extract mean cortical thickness, surface area of an ROI I created with some clusters that showed some group difference. I already have the ROIs I need. What is the easiest way to extract mean values of ROI from all the subjects? Thanks, Sabin

[Freesurfer] wm edit freeview

Dear all, Is there any documentation on doing em edit using freeview. Thanks, SK ___ 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

Re: [Freesurfer] control point guidance

Hi Michael, I had the same problem too. It might be because of the type of scanner you are using. I added -washu_mprage flag, it pretty much helped me (I did not had to add a lot of controls points and so on so forth. You can go through the link below. https://mail.nmr.mgh.harvard.edu/pipermail//f

[Freesurfer] -mprage flags

Hi all, What does -washu_mprage and -mprage flags do in autorecon step. How does it help in segmentation? -SK ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in th

[Freesurfer] longitudinal processing (base-tps error)

HI all, I ran longitudinal processing with reco-all -base -tp -tp -all but in base-tps file of template ID I found the subject ID of MRI_T1 twice instead of MRI_T1 and MRI_T2. I want to run recon-all -long which I am able to do for MRI_T1 but could not do the same for MRI_T2. ANy help would be

[Freesurfer] longitudinal processing for lgi comparison

Hi all, Is there a longitudinal processing stream to compare local gyrification index (lgi) across two time points. -Sabin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The inform

[Freesurfer] longitudinal analysis subcortical volumes

Hi all, Just to be sure, if I want to compare ICV or hippocampus volume between two time points I extract the values from aseg.stats of MRI_001.long.template and MRI_002.long.template right. Also, if thats the case is it okay if I rerun autorecon with -hippo-subfields flags for those MRI_001.long.

[Freesurfer] long.qdec.table.dat question

Hi all, I am trying to use qdec to perform comparison of cortical thickness in two different time periods. So I ran recon-all base and recon-all -long. then defined long.qdec.table.dat as fsid fsid-base years MRI_001_T1 MRI_001 0 MRI_001_T2 MRI_001 2 When I