[Freesurfer] freesurfer pipeline for sub mm voxel resolution

Hi All, I am working with some 7T data with 0.7 mm isotropic voxels and wanted to know if free surfer pipeline (version 5.3) can work these images ? I also have FLAIR images and wanted to know if I can use the two to create myelin maps ? Please suggest. Thanks Ri ___

[Freesurfer] lobar volumes (gm and wm combined)

Hello All, I am interested in calculating volumes of the frontal / temporal / parietal / occipital lobes, gm and wm combined for each lobe. Is there a quick way to do that or do I have to add the cortical and the wm volumes for all the substructures of each lobe to get the total volume for eac

[Freesurfer] white and pail surface editing

Hi All, We have some subjects who have both wm errors and gm errors. Is the following workflow possible Step 1) control points for the white matter edits. DONT RUN recon-all Step 2) add the pial surface edits. DONT RUN recon-all Step 3) Run recon-all to incorporate control points for wm edit

[Freesurfer] DTI of frontostriatal tracts

Hello All, We are studying adolescents with HIV and are interested in frontostriatal tracts (anything from frontal cortex to caudate/putamen/nucleus accumbens) and tracts connected to the amygdala. Is anyone aware of DTI based atlases where these tracts are defined in MNI or some other standa

Re: [Freesurfer] DTI of frontostriatal tracts

> On 8/2/16 12:26 PM, Ritobrato Datta wrote: >> Hello All, >> >> We are studying adolescents with HIV and are interested in >> frontostriatal tracts (anything from frontal cortex to >> caudate/putamen/nucleus accumbens) and tracts connected to the amygdala. &

[Freesurfer] question about cortical volume group analyses

Hi All, I have a analysed data from AD patients and healthy controls and want to do a group analyses of cortical volume. I have run qcache on each subject. In the lh.volume.fsaverage.mris_preproc.log file, mri_surf2surf --srcsubject AD1 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsav

Re: [Freesurfer] question about cortical volume group analyses

Dear All, The email below probably fell through the cracks so I am resending it. Appreciate your thoughts and suggestions. Best Ri - Original Message - From: Ritobrato Datta To: Freesurfer support list Sent: Tue, 17 Jan 2017 14:05:10 -0500 (EST) Subject: question about cortical

[Freesurfer] T1 FLASH parameters for cortical thickness analyses

Hi All, I have collected T1 3D FLASH on a subject and here are some details of the sequence, Manufacturer = SIEMENS StudyDescription = Neuro_3T^brain_3t SeriesDescription = Axial Global FLASH FA27 ManufacturersModelName = Verio ReferencedImageSequence = 1.2.840.10008.5.1.4.1.1.4\1.3.12.2.1107.5

Re: [Freesurfer] T1 FLASH parameters for cortical thickness analyses

possibility to extract both the measures from a single anatomical sequence. Please let me know. Thanks Rito - Original Message - From: Bruce Fischl To: Ritobrato Datta Cc: free surfer Sent: Tue, 10 Dec 2013 13:42:05 -0500 (EST) Subject: Re: [Freesurfer] T1 FLASH parameters for cortical

[Freesurfer] primary auditory cortex ROI

Hi All, I need to demarcate primary auditory cortex in a group of subjects anatomically and I came across the following papers - https://surfer.nmr.mgh.harvard.edu/ftp/articles/2013/2013_-_Wasserthal_et_al._-_NeuroImage.pdf https://surfer.nmr.mgh.harvard.edu/ftp/articles/Sigalovsky_et_al_2006.p

[Freesurfer] primary auditory cortex ROI

Hi All, My email may have fallen through the cracks over the weekend so I am sending it again. I need to demarcate primary auditory cortex in a group of subjects anatomically and I came across the following papers - https://surfer.nmr.mgh.harvard.edu/ftp/articles/2013/2013_-_Wasserthal_et_al.

Re: [Freesurfer] primary auditory cortex ROI

ROI We do have a label for transversetemporal. What do you want to do with it? You can extract it out of ?h.aparc.annot or aparc+aseg.mgz, depending on what you want to do with it doug On 03/08/2014 06:48 AM, Ritobrato Datta wrote: > Hi All, > > I need to demarcate primary auditory co

Re: [Freesurfer] HSF in 5.3

Hello All, I have run my data through free surfer 5.1. If I run recon-all distributed with free surfer 6 as follows /Applications/freesurfer6/bin/recon-all -s bert -brainstem-structures where bert was created using freesurfer 5.1, will it work ? Best Ri - Original Message - From: Eu

[Freesurfer] freesurfer 6 error: dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib

Hello All, I installed freesurfer 6 on a mac running OS-X Yosemite 10.10.4. I am getting the following error when I run recon-all from freesurfer 6. Can you please suggest how to fix it ? Thank you, Ri ri@Magi [0] ~/ri/SampleDatasets$ export FREESURFER_HOME=/Applications/freesurfer6;export

[Freesurfer] reference for using T2 to improve pial surface

Hi All, Can someone point to a reference which shows the advantage of using T2 alongside T1 to improve the gray - pial boundary ? Thank you, Ri ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listin

[Freesurfer] question abt optic chaism volume

Hi All, I am using freesurfer 5.1 for my analysis. In FS 5.1, does the Supratentorial volume include the Optic chaism volume ? Please let me know. Thanks Ri ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu

[Freesurfer] brain parenchymal fraction calculation

Hi All, I am using freesurfer 5.1 and I want to compute the brain parenchymal fraction (GM+WM/GM+WM+ventricularCSF). In aseg.stats, I get the whole GM vol and I can also get the total ventricular CSF by adding the vols of different ventricles. But I am confused abt the terminology - Cortical

[Freesurfer] question abt dt-recon

Hello All, I havent used dt-recon yet but I have a question abt it. When the dt-recon computes the FA maps, whats the dimensions of these FA maps ? Are they resampled to the freesurfer anatomical voxel size (1x1x1) or are they in their native voxel size (in which they were collected) ? If I wa

[Freesurfer] question abt supratentorial vol and total brain vol.

Hello All, I am using freesurfer 5.1 for my analysis. I am interested in calculating the whole brain vol (total Gray vol + total WM vol) excluding the CSF volume and cerebellum. Total Brain Vol = TotalGrayVol + CorticalWhiteMatterVol In all of the 79 subjects, when I compare the Total Brain

[Freesurfer] Repost: question abt supratentorial vol and total brain vol.

Hello All, Can someone address the following ? I sent this query yesterday but it fell through the cracks. I am using freesurfer 5.1 for my analysis. I am interested in calculating the whole brain vol (total Gray vol + total WM vol) excluding the CSF volume and cerebellum. Total Brain Vol

Re: [Freesurfer] Repost: question abt supratentorial vol and total brain vol.

somewhere which specifies which of these freesurfer parcellated structures contribute to these combined measures such has supratentorial vol / whole gm vol etc etc That will be very helpful. - Original Message - From: Douglas N Greve To: Ritobrato Datta , Freesurfer

Re: [Freesurfer] Repost: question abt supratentorial vol and total brain vol.

subtract "anything not in WM". It is approximately equal to the count of WM voxels in aparc+aseg.mgz. Since, cerebellar wm is in the aparc+aseg.mgz so that means its included in the CorticalWhiteMatter, correct ? - Original Message - From: Douglas N Greve To: Ritobrato

Re: [Freesurfer] Repost: question abt supratentorial vol and total brain vol.

mri_segstats on the data that has been run through 5.1, will it generate this volume ? Please let me know and sorry to keep pestering this. Thanks Rito - Original Message - From: Douglas N Greve To: Ritobrato Datta Cc: Freesurfer@nmr.mgh.harvard.edu Sent: Mon, 03 Jun 2013 13:54:01 -0400

[Freesurfer] color table for custom labels

Hello All, I have created some labels and want to assign distinct colors to each and save it so that I can assign the same colors when I load them again. How do I do it ? Thanks Ri ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://m

[Freesurfer] masking ?h.curv with a label

Hi, I have created a ?.cortex.label on canine brain. How do I apply this label to the ?h.curv and ?.sulc so that I get rid of the medial wall FOREVER ? Thanks a lot Ri ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.har

[Freesurfer] tkregister2 error on lion

Hi All, I have freesurfer 5.1 installed on my laptop running Lion. When I tried to use tkregister2, the program doesnt load up the GUI. It failed even after installing XQuartz. It loaded successfully in a machine running Snow Leopard. Any suggestions on how to get around it or are there any fi

[Freesurfer] optic radiation ROI

Hi All, Is there an Optic Radiation ROI in freesurfer or some other program ? Please let me know. Thank you Ri ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in

Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0

I concur. I have seen similar results in primary visual cortex from ~40 subjects. While fs 5.1 estimated mean thickness in the range of 1.5 to 1.9 in V1, fs 5.2 is giving me V1 thickness in the range of 2 to 2.3. Ritobrato Datta, Ph.D. Post Doctoral Researcher Department of Neurology University

Re: [Freesurfer] Mindboggle official software release and publication!

Hi Arno, This is fascinating stuff. In my research, I have come across instances when I felt that a hybrid of ANTS and freesurfer would be very useful. Is this pipeline possible for data processed with the earlier versions of freesurfer say 5.1 ? FS6 just got released in Jan 2017 and I am sure

[Freesurfer] license file error

Hi All, I am using Mac OS X Sierra and I downloaded free surfer 6 and when running recon I am getting the following error reading from IM-0001-0001.dcm... -- ERROR: Invalid FreeSurfer license key found in license file /Appl

[Freesurfer] dt_recon error

Hi All, I ran dt_recon and got the following error. Can someone suggest how to fix this ? I have attached the dwi-infodump.dat file for more information. Thanks a lot for the help. Best Rito #@#--- Fitting Tensors Mon Aug 11 07:29:29 EDT 2014 cd /Users/iron/rito/V

Re: [Freesurfer] Fwd: V1 and V2 labels valid with clinical populations?

Hi Krista, Please refer to the following publications from Geoff Aguirre's lab - http://www.ncbi.nlm.nih.gov/pubmed/23041195 http://www.ncbi.nlm.nih.gov/pubmed/24676149 All templates are in fsaverage_sym space in .mgh format and are available for download https://cfn.upenn.edu/aguirre/wiki/pu

[Freesurfer] resampling method to transform EPI vol to surf

Hi All, For a reviewer, I need the following ASAP: Comments from Reviewer: Please provide a brief description of the resampling method by which volume data were transformed to surface data. Was the data averaged between the white and pial boundaries? Or was a constant normal average taken? I

Re: [Freesurfer] resampling method to transform EPI vol to surf

ll us how you sample your data onto the surface. Presumably you must have used mri_vol2surf (at least implicitly) to use the resultant registration to sample your data onto the surface. What is the exact command you use? Cheers, Thomas On Tue, Dec 23, 2014 at 7:26 PM, Ritobrato Datta wrote: >

[Freesurfer] outline of a label as an overlay

Hello All, Is there a way to save the outline of a label as an overlay (say .mgh file) ? Please let me know. Thanks Ri ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The inform

[Freesurfer] V1 on fsaverage

Hi Is it possible to estimate the V1 boundary on fsaverage using Hinds method ? Thanks Ri ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is inten

[Freesurfer] Periaqueductal gray ROI

Hi All, Is there a Periaqueductal Gray ROI generated by freesurfer recon ? Please let me know. Thanks Ri ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in th

[Freesurfer] thalamic segmentations in freesurfer

Hello All, I noticed the following in FreeSurferColorLUT.txt 8001 Thalamus-Anterior 74 130 181 0 8002 Thalamus-Ventral-anterior 242 241 240 0 8003 Thalamus-Lateral-dorsal 206 65 78 0 8004 Thalamus-Lateral-pos

Re: [Freesurfer] what is thalamus-proper and clusters-table related question

Actually I have the same question - does the thalamus proper include LGN ? - Original Message - From: "Douglas N Greve" To: "Tetiana Dadakova" Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, September 2, 2011 12:28:45 PM Subject: Re: [Freesurfer] what is thalamus-proper and clusters-tab

[Freesurfer] distortion metric question

Hi All, Is there a way to examine the distortion metric of the freesurfer surface normalization ? Please let me know. Thanks Ri ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer T

[Freesurfer] defining our own regions for tractography

Hello All, I am a total newbee in dt-recon and tracula. So sorry if this is a very basic question. >From what I gathered so far- TRACULA uses the aparc+aseg.mgz from the FreeSurfer recon (T1-weighted volume) as ROIs to construct the tracts and also constructs a few tracts by default. Is ther

[Freesurfer] normalised functional volumetric data to fsaverage

Hi All, I have some functional beta maps normalised to the T1 template using spm8 and I am wondering how to map them onto the fsaverage surface ? In native subject space, I pipe a functional scout image into bbregister to get a registration matrix which is then used to map volumetric beta maps

[Freesurfer] dividing a label into equal parts

Is there a way to divide a surface label like V1 into equal parts (say 10 parts) either along its length or width and save each part as a separate label ? Drawing them in tkmedit is quite crude and not very accurate. Please let me know. Thanks Ri __

[Freesurfer] error while dividing an annotation/label

Hello, I am trying to divide lh.v1.predict.label into equal parts. So I did the following - A) Created a colorfile V1color.ctab which contains the following- # #No. Label Name:R G B A 1 V170 130 180 1 B) mris_label2ann

[Freesurfer] setting a cluster size and thresholding in tksurfer

Hi I am displaying the fMRI results in tksurfer. Is there a way in tksurfer to set a cluster size (for eg 50 vertices) and display only those activated regions which have bigger clusters than 50 ? Thanks Ri ___ Freesurfer mailing list Freesurfer@nmr.

[Freesurfer] length of a label

Hi All, Is there a way to calculate the length and width of a label ? Please let me know. Thanks a lot Ri ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in thi

[Freesurfer] question abt flattening in freesurfer

Hi All, My name is Ritobrato Datta and I am a post-doc at PENN. I have just started learning Freesurfer. I am trying to create occipital flatmap in freesurfer using the command mris_flatten. I followed the commands as described but am getting the following error. I created the lh.occip.patch

[Freesurfer] question abt inflated brain registration

functional data on this "registered inflated brain" ? Please let me know. Thanks Ri Ritobrato Datta, Ph.D. Post Doctoral Fellow Department of Neurology University of Pennsylvania School of Medicine 3rd Floor Gates Building 3400 Spruce St. P

[Freesurfer] running freesurfer after talairach touch-ups...

Hello all, I ran recon-all -autorecon-all -s After it ran all the way through, I ran tkregister2 --mgz --s --fstal --surf orig and saved everything with the SAVE REG button in the tkregister2 toolbar. Since I initially ran all the steps before the talairach touch-ups, what do I run to re

[Freesurfer] read in .vtk files ?

Hello All, Can freesurfer read in .vtk surface files ? Please let me know. Thanks Ri ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Segmentation fault

7 EDT 2009 _ Thanks Ri Ritobrato Datta, Ph.D. Post Doctoral Fellow Department of Neurology Center for Functional Neuroimaging University of Pennsylvania School of Medicine 3rd Floor Gates Building 3400

[Freesurfer] converting .img to .nii

Hello All, I am trying to convert [...@home] /jet/subjects/002/Anatomy> mri_convert nAnatomical_fsl_FLOAT.img nAnatomical_fsl_FLOAT.nii mri_convert nAnatomical_fsl_FLOAT.img nAnatomical_fsl_FLOAT.nii $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from nAnatomical_fsl_F

Re: [Freesurfer] problem with intensity normalization control points

Thx Nick for the reply. Then how do I make sure that the spline (that I have used control points to demarcate) is included in the white matter boundary ? Ri - Original Message - From: "Nick Schmansky" To: "Bruce Fischl" Cc: "Ritobrato Datta" , "fre

[Freesurfer] transforming of the spherical atlas Right --> Left hemisphere ??

Hello All, we are considering combining some data from the left and right hemispheres. Is there a way to implement a transform of the spherical atlas Right --> Left hemisphere? Topologically, this probably corresponds to turning the sphere inside-out (plus registration of residual hemispheric d

[Freesurfer] question abt mri_surf2surf usage

Hello All, I am confused abt the sage of mr_surf2surf. I have 3 subjects. All three have been piped through freesurfer autorecon-all. So i have subj? ?h sphere.reg I also have functional data for the 3 subjects overlaid on the subj? ?h sphere.reg and I saved them as .mgh files. I want to map

[Freesurfer] structural morphometric analyses for 50 subjects

only the changes due to temperature change ? I have never done this kind of an analyses before, so so maybe freesurfer already has a pipe for this sort of analyses. I dont know. I am looking for any guidance I can get. Please let me know. Thanks a lot, Rito Ritobrato Datta, Ph.D. Post

[Freesurfer] talairach failure

Hello All, I ran recon-all on a subject and got the following error talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm # #...@# Talairach Failure Detection Thu Nov 19 16:17:54 EST

[Freesurfer] annot to label to gm thickness map

Hello All, I want to create a gm thickness map from central sulcus and precentral gyrus. I plotted the lh.aparc.a2005s.annot on the inflated surface and I see the sulci and gyri. Is there a way to create a binary label of the central sulcus and precentral gyrus ? Can that label be then used

[Freesurfer] aparcstats2table for std dev associated with av thickness

Hi all Is there a way to create a multi subject table of the std dev associated with av thickness using aparcstats2table or for that matter any way to create a table similar to the outout of aparcstats2table ? Thanks Ri ___ Freesurfer mailing list Fr

[Freesurfer] combining multiple labels to a single label

Hi all, Is there a way / program to specify and combine multiple labels to create a single label ? Please let me know. Thanks a lot Ri ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/frees

[Freesurfer] thickness map from a label

Hello All, I have created some surface labels and want to create corresponding thickness maps (Not stats). Is there a way to do that ? Thanks Ri ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/list

[Freesurfer] commandline tools to create .mgh files from .nii files.....

Hello All, Are there commandline tools to take processed functional data in .nii format and overlay it on the inflated or spherical surface and output a .mgh file ? I want to specify the registration method as "Calculate identity matrix" Thanks Rito _

[Freesurfer] question abt mri_vol2surf....

Hello All, I have a simple question. I have functional data (3 mm cubic voxels) from 20 subjects that I am using mri_vol2surf to resample on the fsaverage surface. I want to run qdec or mri_glmfit on these data. In order to do grp stats with functional data, what surface do I need to specify in

Re: [Freesurfer] question abt mri_vol2surf....

ok thats what i thought but just wanted to double check... Thx - Original Message - From: "Nick Schmansky" To: "Ritobrato Datta" Cc: "freesurfer" Sent: Tuesday, February 16, 2010 12:58:07 PM GMT -05:00 US/Canada Eastern Subject: Re: [Freesurfer] ques

[Freesurfer] LGN label or ROI....

Hi All, Is there a method for obtaining an ROI for the lateral geniculate nucleus in freesurfer ? Thanks, Ri ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] volumetric version of fsaverage brain

Hello All, Which is the volumetric version of the fsaverage brain in freesurfer ? Can you tell me what is it called ? Thanks Ri ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] converting label to binary mask.mgh

Hello All, I have created a V1 label using Hinds and Fischl Method. Is a label a .mgh file as well ?? How do I convert this label to a binary mask mgh file ? Please let me know. Thanks much Rito ___ Freesurfer mailing list Freesurfer@nmr.mgh.harva

[Freesurfer] "--sfmt curv" flag

Hello All, I posted this question yesterday. It probably got lost. So I am posting again. For functional data to be resampled to fsaverage using mri_surf2surf what should be used with " --sfmt " flag ? For the thickness the --sfmt curv is used when running qcache. Thanks Ri

[Freesurfer] question about lesion segmentation using samseg

External Email - Use Caution Hi All, I have T1w MPRAGE, T2w and PD images but I dont have FLAIR images from a Multiple Sclerosis study. Can I use samseg to segment the lesions ? Can you please suggest ? Many thanks Ri ___ Freesurfer m

[Freesurfer] question about longitudinal data analyses

External Email - Use Caution Hi All, I have the following data – I have 205 subjects - each subject was imaged at 3 timepoints (baseline, followup 1 and followup 2) The 205 subjects are split in two treatment arms with 100 subjects in the first one and 105 subjects in the sec

Re: [Freesurfer] question about longitudinal data analyses

? Many thanks Rito On Fri, Jul 9, 2021 at 4:04 PM Douglas N. Greve wrote: > > > On 7/9/2021 11:44 AM, Ritobrato Datta wrote: > > External Email - Use Caution > > Hi All, > > > I have the following data – > > > > I have 205 subjects - each su

Re: [Freesurfer] question about longitudinal data analyses

Mon, Jul 12, 2021 at 10:51 AM Douglas N. Greve wrote: > Yes, it will work on both. If you use a table, then pass the table with > --table tablefile instead of --y > > On 7/12/2021 7:54 AM, Ritobrato Datta wrote: > > External Email - Use Caution > Good morning, > >

[Freesurfer] error running samseg on cluster

External Email - Use Caution Hi All, I am trying to run samseg as follows on a cluster and am getting a message that I need to install tensorflow (which is already installed). Please see below. Please advise how to fix this. Many thanks Rito -

[Freesurfer] impact of defacing on eICV calculations

External Email - Use Caution Hi All, I have inherited some T1 data that are defaced. If I run the defaced images through freesurfer, will that impact the eICV calculations ? Please let me know. Many thanks Ri ___ Freesurfer mailing l

[Freesurfer] occipital label without v1

Hello All, I have an occipital label and a v1 label and I have created binary masks from them. Is there a way to create an "Occipital label - V1 label" ie excluding v1 from occipital label. Please let me know. Thank you Ri ___ Freesurfer mailing lis

[Freesurfer] mask.mgh to volume

Hello All , I have a binary mask - mask.mgh. I want create a binary volumetric mask from it in the same space and dimension as orig.mgz Can mri_label2vol be used ? How ? If not, how can this be done ? Thanks a lot Ri ___ Freesurfer mailing list Fre

[Freesurfer] black background to white in tksurfer

Is there a way to set the black background to white in tksurfer ? Thanks Ri ___ 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 th

[Freesurfer] freesurfer and VBM

Hello All, Are there any papers comparing freesurfer to VBM ? Can anyone point me to them ? Thanks Ri ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-m

[Freesurfer] laterality analysis

Hello All, I am trying to do a laterality analysis for a cortical reorganization project in blind patients. Since each hemisphere has slightly different gyral and sulcal patterns, in theory, one hemisphere could be mirrored and compared; in the surface space this amounts to turning one of the s

[Freesurfer] way to binarize MGH file

Hi All, I am looking for a way to binarize MGH files. I took a mask I made in volumetric space to surface space, and I want to binarize it so it doesnt contain decimal values. What is the command? Will mri_binarize work on mgh files ? I need to manipulate MGH files, with the same output type.

[Freesurfer] effect size for cortical thickness changes

Hello All, Are there reports of studies of cortical thickness changes using freesurfer which report effect sizes for the ROIs of interest ie how much of a change in millimeters was observed as opposed to p-values reported. Please let me know. Thanks a lot Ri __

[Freesurfer] .mgh to .label ??

Hello All, How do I convert an .mgh file (my .mgh file is a binary mask) onto a label ? Is there an automated way other than drawing ? Thanks Ri ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listin

[Freesurfer] different V1 sizes for same subject in two different sessions

Hello All, I have estimated V1 using Hinds and Fischl method for some subjects scanned on two different days. I've been going through the V1 surface area data for these. One thing that concerns me is that is seems that very different V1 sizes are reported for the same subject when scanned on di

Re: [Freesurfer] flattenning question

Continuing the conversation, if I have a flattened patch like an occipital patch, and i manually draw a label on it and save it, can I then use mri_label2label to map it to other subjects ? Thx Ri - Original Message - From: "Bruce Fischl" To: "Gabriel Go.Es." Cc: "free surfer" Sent:

[Freesurfer] question abt fsaverage V1

Hello All, I noticed that that there is a fsaverage/label/?h.V1.label Is this label created from the Hinds and Fischl method ? Can someone give some details abt it ? Also for individual subjects, when I run the V1 estimation using Hinds and Fischl method, how accurate are the V1 / V2 border co

[Freesurfer] stats on masked functional data

Hello All, I have a functional beta value overlay as a .mgh file and a label file and I want to compute the average value within that mask for each subject. Is there a program to do that ? Thanks Ri ___ Freesurfer mailing list Freesurfer@nmr.mgh.har

[Freesurfer] stats on masked functional data

Hello All, Looks like this question slipped through. I have a functional beta value overlay as a .mgh file and a V1 label file and I want to compute the average beta value within that mask for each subject. How do I do this ? Thanks a lot Ri ___ Fr

[Freesurfer] gyrification Index of a label

Hi All, I have run recon-all -s -localGI Now I want to get the gyrification Index of a particular label. Is there a way to do that ? Please let me know Thanks Ri ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.har

[Freesurfer] V1 dimensions

Hello All, Is there a way to calculate the length and breadth of V1 in mm defined by the Fischl method ? How do I do it ? Thanks Ri ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer