Re: [Freesurfer] extract pial surface

Thanks! How can I read/open the file? Best, Sandy Am 06.11.15 um 08:30 schrieb chenhf_uestc: The area.pial file. Best, Feng *发件人：*Sandy Schramm *发送时间：*2015-11-06 15:24 *主题：*[Freesurfer] extract pial surface

Re: [Freesurfer] SNR Tracula

Hi Scott, This previous post might help you. https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg41439.html Best wishes, Barbara On Sun, Nov 8, 2015 at 10:43 PM, Scott Quadrelli wrote: > Hi, > > Tracula outputs the SNR for each volume in a txt file. I was wondering if > anyone can p

[Freesurfer] TRACULA preprocessing error

Dear all, I am running Tracula preprocessing on NIFTI files. After running the command: trac-all -prep -c I get the error: ... processing /data_august/Deniz/freesurfer/traculaoutput/DTI_con_AbSa90/dmri/dwi_tmp0032 mv -f /data_august/Deniz/freesurfer/traculaoutput/DTI_con_AbSa90/dmri/bvecs /data_a

[Freesurfer] ROI

Hi I have created and saved labels for 2 regions in the anterior cingulate and corpus callosum in the left hemisphere and I would like to know if there is a way I can convert my .label files from the lh->rh without drawing them by hand in the other hemisphere. Thanks in advance, Best regards, Ge

Re: [Freesurfer] extract pial surface

Hi Sandy it's in "curv" format, so read_curv.m in matlab would open it for example cheers Bruce On Mon, 9 Nov 2015, Sandy Schramm wrote: Thanks! How can I read/open the file? Best, Sandy Am 06.11.15 um 08:30 schrieb chenhf_uestc: The area.pial file.   Best, Feng    

Re: [Freesurfer] Issues with fsgd g2v1

Dear Heidi, 1. you need to specify --surface for your data, subj is where the surface stack was created, usually fsaverage, and hemi is lh in your case (base on your input name for y). 2. you need to source freesurfer. The license file needs to be in FREESURFER_HOME (a file called .license).

[Freesurfer] mri_surfcluster statistics and label question

Dear FreeSurfer experts, In the output mri_surfcluster (e.g., https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisClusterSummary), what is the statistics behind the Max? Is it either t-statistic (if only 1 line of contrast) or F-statistic (if two lines of contrast), but not Z-sta

[Freesurfer] can't change common-space subject in qdec

Dear Freesurfers: I've encountered the same problem as posted previously by Laura some time ago (see below), I am using qdec 1.5 with freesurfer version 5.3. freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 Basically, I cannot change the common-space subject from the default fsaverage to my o

[Freesurfer] How to compute area of subcortical structures

Hi, I am trying to find how to compute the area of subcortical structures like amygdala, hippocampus, thalamus etc. I have checked stats/aseg.stats file but it doesn't have areas. I looked at mri_asegstats and mris_anatomicalstats commands. Using mris_anatomicalstats I am able to compute surfa

Re: [Freesurfer] recon-all error message

Hi Nicole that's a very strange error. Are you sure that you didn't run out of disk space? Bruce On Mon, 9 Nov 2015, Nicole Zurcher wrote: > Dear all, > > One of my freesurfer recons is failing and I am not sure how to > troubleshoot. > > This is the error message that I get at the end of the r

Re: [Freesurfer] How to compute area of subcortical structures

Hi Anirudh you could tesselate them (using mri_tesselate or mri_ic) then compute the surface area of the tesselation, although this will be an overestimate due to the Cartesion voxels. We don't typically compute surface area of subcortical structures since volume is what people are more intere

Re: [Freesurfer] TRACULA preprocessing error

Hey D, I also had the same error in the same spot, although I'm using an earlier version of tracula and Mac OS. This is my first time using tracula for DWI processing so I am a little confused as to how to best troubleshoot this issue. Any help from the experts would be great! Thanks, Doug

[Freesurfer] Research Scientist job in fMRI data analysis

New York University is looking for an Assistant Research Scientist who will work with faculty in the Center for Brain Imaging (CBI) to help implement analysis techniques, establish data analysis streams, and to make state-of-the-art MR techniques such as multi-echo/multi-plexed BOLD fMRI, diffu

Re: [Freesurfer] TRACULA preprocessing error

Hi Douglas, I actually solved it! So, if yours is the same problem, you need to change your bval and bvec file format. I used mricron to convert from dicom to nifti, then used the bvec and bval files it produced for me. What it gives as output doesn't match with tracula's format. bvec file should

[Freesurfer] convert label to mgh

Dear FreeSurfer Experts, Is it possible to convert a label file to a surface-based mgh file? Could you please provide an example (e.g., on a white surface)? Best, Daniel -- Daniel Yang, Ph.D. Yale Child Study Center E-mail: daniel.yj.y...@yale.edu ___

Re: [Freesurfer] convert label to mgh

use mri_label2label with the --mask option On 11/09/2015 01:34 PM, Yang, Daniel wrote: > Dear FreeSurfer Experts, > > Is it possible to convert a label file to a surface-based mgh file? > Could you please provide an example (e.g., on a white surface)? > > Best, > Daniel > -- > Daniel Yang, Ph.D.

Re: [Freesurfer] Drawing a circle around a vertex on a surface

One way is to create a surface overlay with the target vertex = 1 and other vertices 0 (mri_volsynth, use delta, works for surface overlays too). Then smooth by a certain FWHM (mri_surf2surf or mris_fwhm). This will create a circle. If you divide all vertices by the value of the vertex after sm

[Freesurfer] mri_surf2surf - Interpolation

Hello all, I'm in the process of mapping some non-FreeSurfer derived outcomes to a curv file containing the vertices of the pial surface mesh. I have values at roughly 100 vertices, leaving some 37000 with 'nan'. I then run an intra-subject surf2surf command in an attempt to interpolate betwee

Re: [Freesurfer] convert label to mgh

Hi Doug, Thanks a lot! The --outmask option appears to be working well!! Best, Daniel -- Daniel Yang, Ph.D. Yale Child Study Center E-mail: daniel.yj.y...@yale.edu On 11/9/15, 1:47 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N Greve" wrote: >use mri_label2label with

[Freesurfer] registration format conversion

Hi, I understand lta_convert can generalize between FSL (.mat), tkregister2 (.dat) and FreeSurfer 5 (.lta) format registration matrices. How can I get this file? The location archived in *Re: [Freesurfer] Lta_convert *is no longer available. stephen *stephen v. shepherd phd* The Rockefeller

Re: [Freesurfer] Drawing a circle around a vertex on a surface

Thanks Doug! I also found another solution from you in this post: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-July/031726.html Reza One way is to create a surface overlay with the target vertex = 1 and other vertices 0 (mri_volsynth, use delta, works for surface overlays too). T

Re: [Freesurfer] TRACULA preprocessing error

Hello D, Thanks for the advice! Your suggestion did the trick! I remember reading about properly formatting the bval/bvec files, but I apparently forgot to do so... Thanks, Doug Douglas Merkitch Neurological Sciences Rush University Medical Center Phone: (312) 563-3853 Fax: (312) 563-4660 Ema

Re: [Freesurfer] Drawing a circle around a vertex on a surface

that will work too, but you can't control the radius like you can with my new solution :) On 11/09/2015 04:22 PM, Reza Rajimehr wrote: > Thanks Doug! I also found another solution from you in this post: > https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-July/031726.html > Reza > One w

Re: [Freesurfer] registration format conversion

try this one (for linux) ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/lta_convert On 11/09/2015 03:42 PM, S.V.Shepherd [work] wrote: > Hi, > > I understand lta_convert can generalize between FSL (.mat), > tkregister2 (.dat) and FreeSurfer 5 (.lta) format registration > matric

Re: [Freesurfer] R: Re: R: Re: R: Re: error MRS voxel as seed in FS-FAST

So that mask has 22926 non-zero voxels? The only other thing I can think of is that the registration is off. Have you checked that? On 11/06/2015 07:16 AM, std...@virgilio.it wrote: > I hope that this information are fine > > fslinfo $SUBJECTS_DIR/Control22/MRS_MASK.nii.gz > data_type FLOAT3

Re: [Freesurfer] MNI coordinates for regions in aparc+aseg.mgz file

here is one way mri_cor2label --i aparc+aseg.mgz --id 10 --l left-thal.label mri_label2label --srclabel ./left-thal.label --srcsubject subject --trgsubject talairach --regmethod volume --trglabel left-thal.mni305.label There will be an entry for each voxel in the label. The corrdinates in left

Re: [Freesurfer] node coordinates

you can try a modification of the method that I just sent out. In this case you are dealing with surface ROIs, so Use mri_annotation2label to create labels of each annotation, then mri_label2label --srclabel ./your.label --srcsubject fsaverage --trgsubject talairach --regmethod volume --trglabel

Re: [Freesurfer] hello freesurfer developer~

Hi, please create a new thread since this is a new topic. Also, I don't understand your question so please elaborate. On 11/09/2015 05:34 AM, A-reum Min wrote: > Hello experts! > > i have some question to you.. > > How can i control the cluster size? > > My cluster threshold is 1. > > then, too m

Re: [Freesurfer] ROI

You'll have to run the interhemispheric analysis first. See https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi When that is finished, contact me again and I'll tell you how to transfer the labels On 11/09/2015 07:51 AM, UQAM wrote: > Hi > > I have created and saved labels for 2 regions in the ant

Re: [Freesurfer] R: Re: R: Re: R: Re: average z-score of each subject from a common cluster

On 11/07/2015 07:29 PM, std...@virgilio.it wrote: > Thanks. But what's meaning "colheader"? Column header. The title of the column > In my cache.th13.neg.sig.masked.nii.gz I have only a significant ROI. > In the summary file there are five column and 5 different value of > "mean". > Which is the

Re: [Freesurfer] Two recons with different vertex coordinates

The node list is different so there are a different number of vertices and the vertices do not mean the same thing. Use mri_label2label to map across FS recons even if they are the same subject On 11/08/2015 03:46 AM, Reza Rajimehr wrote: > Hi, > > We have run recon-all twice on a single subject

Re: [Freesurfer] mri_surfcluster statistics and label question

On 11/09/2015 10:51 AM, Yang, Daniel wrote: > Dear FreeSurfer experts, > > In the output mri_surfcluster (e.g., > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisClusterSummary), > > what is the statistics behind the Max? > > Is it either t-statistic (if only 1 line of contra

Re: [Freesurfer] mri_surf2surf - Interpolation

Sounds like you are trying to do soap bubble interpolation (?). I don't think we have a binary for that. Maybe Bruce knows of one. You could hack something together, with smoothing (mri_surf2surf), creating binary masks (mris_binarize), and masking (mri_mask), and basic math operations (fscalc

Re: [Freesurfer] mri_surfcluster statistics and label question

Hi Doug, Got it! Sorry that I keep forgetting this. So it’s an exponent statistic. The reviewers asked for a statistic and df. I think I can convert it to a Z-statistic so it’s more “conventional”. I also noticed that qdec provides a df when I set up the model. It is valid to use that df to deri

[Freesurfer] R: Re: R: Re: R: Re: R: Re: average z-score of each subject from a common cluster

I have run cat ... /my-glm.wls/group.diff/cache.th13.neg.sig.cluster.summary obtained ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZCWP CWPLowCWPHi NVtxs Annot 1 -3.595 110577865.93 11.8 39.4 -0.1 0.00620 0.00520 0.00720 1672 rostralanteriorci

[Freesurfer] unpacksdcmdir

Hi all, I am using unpacksdcmdir to unpack our data (collected using a Siemens scanner) but running into an error. I have two questions and hope someone can kindly help me with them: 1. Why can not I successully unpack images for run10? 2. I got the DTI.nii image, the bvecs and bvals for run4

[Freesurfer] Error: dimension mismatch between source and mask

Dear FreeSurfer experts, After running the following command: recon-all -autorecon2 -autorecon3 -subjid S08_FS I get the following error: /Volumes/FLYNN/ProjetPhonoBehavioralTMS/Freesurfer/S08_FS/mri \n mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz \n threshold mask volume at 5 E

Re: [Freesurfer] mri_surf2surf - Interpolation

there used to be something built into tksurfer to do soap bubble smoothing. You can try smooth_vals_spare from the tcl prompt. I think it depends on setting the fixedval field in the vertex struct to 1 for the stationary points of the soap bubble. You can first read in a file that is 1 for the

[Freesurfer] mri_glmfit fsgd and matrix problems

Hi Freesurfer group - I am receiving errors each time I try to run mri_glmfit. It appears to be the way I set up either the fsgd or mtx file. Any assistance would be greatly appreciated. Thanks, Chaz Hypothesis for the contrast in the mtx file: Is there an average affect of heat threshold regr

Re: [Freesurfer] mri_surfcluster statistics and label question

There should be a t.mgh file there (or maybe F.mgh). You can just pull the value out of the vertex out of that. On 11/9/15 6:46 PM, Yang, Daniel wrote: > Hi Doug, > > Got it! Sorry that I keep forgetting this. So it’s an exponent statistic. > > The reviewers asked for a statistic and df. I think

Re: [Freesurfer] unpacksdcmdir

On 11/9/15 7:41 PM, Li, Baojuan wrote: Hi all, I am using unpacksdcmdir to unpack our data (collected using a Siemens scanner) but running into an error. I have two questions and hope someone can kindly help me with them: 1. Why can not I successully unpack images for run10? Looks like the

Re: [Freesurfer] mri_glmfit fsgd and matrix problems

It looks like you have created your fsgd file using a windows computer. Try running cat file.fsgd | sed 's/\\r/\\n/g' > new.file.fsgd probably have to do the same with the contrast matrix file On 11/9/15 9:18 PM, Gay,Charles Wysaw wrote: Hi Freesurfer group - I am receiving errors each ti