[Freesurfer] recon failed with aseg.mgz

Hi All, The recon-all stopped at the step of mri_normalize. The command is: mri_normailze -mprage -noconform -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz. The error massege: assuming input volume is MGH (Van der Kouwe) MP-RAGE. not interpolating and embedding volume to be 256^3…

[Freesurfer] Register.dof

Hi, I like to transfer a epi file to a T1 space. Is it possible? Thanks, Xiaomin On Tue, Feb 17, 2015 at 1:13 PM -0800, "Douglas Greve" wrote: We don't have anything to do this directly. However, we do have this tool: http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi See if that meets your ne

Re: [Freesurfer] Register.dof

o. It will also resample to the T1 space, but you can also use mri_vol2vol to do so too. doug On 2/18/15 5:43 PM, Xiaomin Yue wrote: Hi, I like to transfer a epi file to a T1 space. Is it possible? Thanks, Xiaomin On Tue, Feb 17, 2015 at 1:13 PM -0800, "Douglas Grev

[Freesurfer] Lta_convert

Hi, Is it possible to download lta_convert? Thanks, Xiaomin On Thu, Feb 26, 2015 at 9:35 AM -0800, "David Grayson" wrote: ok, great. so let's say I have a linear transformation or a full warp field to go between the freesurfer processed image and the unprocessed brain. is there a way that I

[Freesurfer] freeview registration

Hi All, After using freeview to manually adjust the registration between a functional and T1.mgz generated by bbregister, I saved the registration file in freeview as lta format, which seems the only option. However, the registration file has same file name for source and target volume. So, wh

Re: [Freesurfer] freeview registration

se it to check the regsitration, but us tkregister if you need to edit it. doug On 2/27/15 10:18 AM, Xiaomin Yue wrote: Hi All, After using freeview to manually adjust the registration between a functional and T

Re: [Freesurfer] Lta_convert

Thanks Xiaomin On Mon, Mar 2, 2015 at 11:51 AM -0800, "Douglas N Greve" wrote: try this ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/lta_convert On 02/26/2015 12:48 PM, Xiaomin Yue wrote: > Hi, > > Is it possible to download lta_convert? >

Re: [Freesurfer] Register.dof

Thanks. The new freeview can create correct register file Xiaomin On Mon, Mar 2, 2015 at 11:06 AM -0800, "Douglas N Greve" wrote: On 02/18/2015 09:54 PM, Xiaomin Yue wrote: > Hi Doug, > > Thanks for your response. I did run bbregister to register the EPI to > T1, b

[Freesurfer] fs-fast analysis on a group averaged surface

Hi All, I generated a group averaged surface using make_average_surface successfully. Currently, I like to process the fMRI data using this group surface, instead of fsaverage, using the fs-fast pipeline. For doing so, I need to run rawfunc2surf-sess with a parameter where I can input this gr

Re: [Freesurfer] fs-fast analysis on a group averaged surface

Thanks very much. Xiaomin > On Apr 13, 2015, at 9:43 AM, Douglas Greve wrote: > > Use the (undocumented) -trgsubject flag > >> On 4/6/15 9:10 AM, Xiaomin Yue wrote: >> Hi All, >> >> I generated a group averaged surface using make_average_surface &g

[Freesurfer] mri_vol2vol

Hi Doug, I like to convert a native functional data into the anatomical space using mri_vol2vol with --fstal, so that the resample data has same spatial resolution as the original function data. However, mri_vol2vol give a error: --fstal unknown. I also tried using --fstalres as suggested in t

Re: [Freesurfer] mri_vol2vol

starg On 4/14/15 11:36 AM, Xiaomin Yue wrote: Hi Doug, I like to convert a native functional data into the anatomical space using mri_vol2vol with --fstal, so that the resample data has same spatial resolution as the ori

Re: [Freesurfer] mri_vol2vol

that? On 4/14/15 8:20 PM, Xiaomin Yue wrote: Thanks for your response. The command you gave will generate a new function data with the spatial resolution of the anatomical data, which in my case is much higher than those of functional

Re: [Freesurfer] mri_vol2vol

original functional? On 4/14/15 10:30 PM, Xiaomin Yue wrote: yes, that's precisely what I want. the reason is the following. A subject was scanned multiple times across days with slightly different slice position for each time. What I

[Freesurfer] a mkanalysis-sess question

Hi, I have a question related to how to make an appropriate design matrix using fs-fast 5.3. Subjects’ eye movement was collected during an experiment. Then, the data has been transformed to a continuous variable with a number for each TR. The better fixation performance

Re: [Freesurfer] a mkanalysis-sess question

variable or task? In any event, I would probably recode it to make fixation=0 and non-fixation something else On 5/2/15 5:34 PM, Xiaomin Yue wrote: Hi, I have a question related to how to

[Freesurfer] out of memory, fast_selxavg3.m

Hi, I hope that I can get some answers for the question that has been asked previously. I am analyzing a large dataset, which has 28917 time points. Although our server has 128G memory, it is still no enough to process the dataset using fsfast 5.3. One

Re: [Freesurfer] a mkanalysis-sess question

me 1 doug On 5/3/15 11:17 AM, Xiaomin Yue wrote: > Hi Doug, > > Thanks for your response. I want to treat it as a nuisance variable. > If so, should the #3 is best choice? > > Xiaomin > > > Date:

Re: [Freesurfer] out of memory, fast_selxavg3.m

ou can resample with 3 mm (instead of 2 or 1mm). On Sun, May 3, 2015 at 7:57 PM, Xiaomin Yue wrote: > Hi, > > I hope that I can get some answers for the question that has been asked > previously. I am analyzing a large dataset, which has 28917 time points. > Although our server h

Re: [Freesurfer] a mkanalysis-sess question

create a text file with a value for each time point and put it in the run folder then run mkanalysis-sess with -nuisreg filename 1 doug On 5/3/15 11:17 AM, Xiaomin Yue wrote: Hi Doug, Thanks for your response. I want to treat it as a nuisance variable. If so, should the #3 is bes

[Freesurfer] beta value

Hi, During the processing of functional data, can fsfast generate outputs of the significants for each beta values modeled in the design matrix? Thanks,XIaomin___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] beta value

Do you mean by contrasting a condition vs fixation? Xiaomin On Mon, May 18, 2015 at 7:07 AM -0700, "Douglas Greve" wrote: Yes, but you have to set up the contrasts, it won't do it automatically On 5/16/15 10:48 PM, Xiaomin Yue wrote: > Hi, > > During the processing

Re: [Freesurfer] beta value

Thanks Xiaomin On Mon, May 18, 2015 at 9:15 AM -0700, "Douglas Greve" wrote: yes On 5/18/15 10:38 AM, Xiaomin Yue wrote: > Do you mean by contrasting a condition vs fixation? > > Xiaomin > > > > > On Mon, May 18, 2015 at 7:07 AM -0700, "Douglas Gr

[Freesurfer] fast_selxavg3.m

Hi, I am using v5.3 fsfast to analyze a function data. The sexlavg3-sess had this error: ConList=splitstring('XXX') Error: A matlab string constant is not terminated properly (where 'XXX represents contrasts generated using mkcontrast-sess).; | Error: unexpected matlab expression; Error: the i

Re: [Freesurfer] fast_selxavg3.m

: not sure what to tell you. Is there a critical number that causes it to fail? Eg, 400? Or a particular contrast name? I assume that none of the contrast names have a space in them. On 07/09/2015 10:06 AM, Xiaomin Yue wrote: > Hi, > > I am using v5.3

[Freesurfer] Fafast and matlab question

Dear all,   I loaded the t.nii under a contrast directory in freeview, and then loaded the t.nii to matlab using MRIread.  When I checked the t value for a point, such as 32, 38, 32, the value is 3.96.  Then I got value from the same point (32, 38, 32) in matlab,  I got a different t value.  I a

[Freesurfer] mkanalysis-sess, timewindow

Hi, I set timewindow to 10 in the mkanalysis-sess. When I loaded Xtmp.mat in to maltlab, then plot(flac.ev(2).Xirf), the size of the flac.ev(2).Xirf is 20 points, which is corrected because of psdwin is [0 40 2]. Should the psdwin be [0 10 2]? No matter what value I put in to timewindow, t

Re: [Freesurfer] mkanalysis-sess, timewindow

lysis-sess command > > On 08/05/2015 04:17 PM, Xiaomin Yue wrote: > > Hi, > > > > I set timewindow to 10 in the mkanalysis-sess. When I loaded Xtmp.mat > > in to maltlab, then plot(flac.ev(2).Xirf), the size of the > > flac.ev(2).Xirf is 20 points, which is corr

Re: [Freesurfer] mkanalysis-sess, timewindow

; From: gr...@nmr.mgh.harvard.edu > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] mkanalysis-sess, timewindow > > it would be helpful to have your mkanalysis-sess command > > On 08/05/2015 04:17 PM, Xiaomin Yue wrote: > > Hi, > > > > I set time

Re: [Freesurfer] mkanalysis-sess, timewindow

urfer] mkanalysis-sess, timewindow > > it would be helpful to have your mkanalysis-sess command > > On 08/05/2015 04:17 PM, Xiaomin Yue wrote: > > Hi, > > > > I set timewindow to 10 in the mkanalysis-sess. When I loaded Xtmp.mat > > in to maltlab, then plot

Re: [Freesurfer] mkanalysis-sess, timewindow

The psd window is only really relevant for FIR analyses. You are assuming a shape to the HRF (a gamma function), and so FSFAST hard codes the psdwin. If you really want to force it to change, put -timewindow after -gammafit On 8/6/15 4:38 PM, Xiaomin Yue

[Freesurfer] selxavg3-sess, -svres

Hi Doug, In order to understand my data better, I did the following analysis. First, I did a full model analysis with all stimuli conditions included in the analysis using: mkanalysis-sess -fsd bold -paradigm xy_mky_category_eye_weights.par -event-related -refeventdur 1 -no-inorm -delay 0 -poly

Re: [Freesurfer] selxavg3-sess, -svres

variation. Welcome to fMRI:). I think the reason why the residual does not equal y - X*beta is that they are whitened. Try it with whitening turned off and see if you get the same (identical) result. doug On 8/9/15 10:50 PM, Xiaomin Yue wrote:

[Freesurfer] mri_glmfit-sim error

Hi, I got this error when run mri_glmfit-sim: missing name for redirect. I am running freesurfer 5.3. the command is: mri_glmfit --glmdir ces.nii --cache 2 --sim-sign . The ces.nii was generated from group level analysis (isxconcat-sess). Thanks for your help. Xiaomin

Re: [Freesurfer] mri_glmfit-sim error

Thanks Xiaomin On Tue, Sep 8, 2015 at 2:03 PM -0700, "Douglas N Greve" wrote: Use "abs" not "" On 09/04/2015 03:20 PM, Xiaomin Yue wrote: > Hi, > > I got this error when run mri_glmfit-sim: missing name for redirect. > I am running freesurfer

[Freesurfer] Retinotopy questions

Hi, I am running a retinotopy analysis using fsfast 5.3.  The design has 15 TR blank before and after wedge presented for 30 TR with 7 repeats, and ring presented  for 24 TR with 7 repeats.  Here is my analysis: mkanalysis -s vz -a rtoy.self.rh -fsd bold -fwhm 2 -nskip 15 -TR 1.5 -retinotopy 48

[Freesurfer] a retinotopy question

Hi All, During the experiment, a wedge was presented clockwise, starting from the low vertical meridian, and a ring was presented from center to peripheral. The analysis done successfully with fs5.3 generated values of polar angle and eccentricity for each voxel. For example, the voxel A has

[Freesurfer] B1 correction

Hi, B1 field correction was collected during the scan. My question is how it can be used in the surface reconstruction? Thanks, Xiaomin Yue ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

[Freesurfer] fsfast question

conditions in the steps of generating design matrix? If so, what command should be used? Thanks,Xiaomin Yue___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo

Re: [Freesurfer] B1 correction

-0400 From: fis...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] B1 correction Hi Xiaomin can you be more specific? What kind of B1 field map did you collect? Do you mean B1 transmit or receive? cheers Bruce On Mon, 24 Mar 2014, Xiaomin Yue wrote: >

Re: [Freesurfer] B1 correction

thanks. Xiaomin Yue Date: Wed, 26 Mar 2014 11:54:58 -0400 From: fis...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] B1 correction Hi Xiaomin do you mean dividing by the Jacobian of the B0 unwarping field? Are you sure it's not B1? That is by far the

Re: [Freesurfer] fsfast question

rvard.edu > Subject: Re: [Freesurfer] fsfast question > > > Sorry, I don't follow what you are asking. FSFAST does not do any drift > removal from the raw data, all of that is in the design matrix > doug > > On 03/26/2014 10:45 AM, Xiaomin Yue wrote: > > Hi, >

Re: [Freesurfer] B1 correction

Hi Bruce, You are correct that it is B1. How could I incorporate this data into the reconstruction stream? Thanks,Xiaomin From: yu...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] B1 correction Date: Wed, 26 Mar 2014 13:54:37 -0400 thanks. Xiaomin Yue Date: Wed

Re: [Freesurfer] fsfast question

, then run selxavg3-sess with -no-con-ok and -svres to save the residuals. maybe that solves your problem? caspar 2014-03-26 14:38 GMT-04:00 Douglas N Greve : No, sorry On 03/26/2014 01:54 PM, Xiaomin Yue wrote: > I like to regress out the linear drift, mean, and head motion > gen

[Freesurfer] recon error

GMT-04:00 Douglas N Greve : No, sorry On 03/26/2014 01:54 PM, Xiaomin Yue wrote: > I like to regress out the linear drift, mean, and head motion > generated by the motion correction step of fsfast from the raw time > course only. Is it possible using fsfast? > > Xiaomin > >

[Freesurfer] recon error

execution aborted Any idea what could be the cause? Thanks,Xiaomin Yue ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard

[Freesurfer] recon all with 7T data

ional parameter: -use-mritotal. My question is how the -use-mritotal parameter would affect final surface? Thanks for providing your input on this. Xiaomin Yue ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] recon all with 7T data

this page for more info: > http://freesurfer.net/fswiki/talairach?highlight=%28use%5C-mritotal%29 > > > -jon > > > > > > > > On Fri, 28 Mar 2014, Xiaomin Yue wrote: > > > > > I tried to do surfer reconstruction (version 5.3) collected

Re: [Freesurfer] recon all with 7T data

try to follow the first few steps of the HiresRecon (http://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon). The parameters of the inhomogeneity correction are optimized for 7T data which should help in reducing errors due to strong bias fields. Best,Falk Von: Xiaomin Yue Gesendet: ‎Mittwoch‎, ‎2‎

[Freesurfer] freeview and ?h.cortex.patch.flat

Hi, Can the developmental freeview display ?h.cortex.patch.flat? I can't find answers in the mail list. If not, is there any way to convert the patch.flat to a format freeview can display? Thanks,Xiaomin___ Freesurf

Re: [Freesurfer] freeview and ?h.cortex.patch.flat

Patch -> LoadPatch and choosing the correct patch.flat file. These instructions are detailed here: https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#Flattening Best, Lee On Thu, 1 Oct 2015, Xiaomin Yue wrote: > Hi, > Can the developmental freeview display ?h.cortex.patch.flat? I can't

Re: [Freesurfer] mri_surf2vol {Disarmed}

el even if only a corner of it has some surface in it. On 01/15/2016 12:16 PM, Xiaomin Yue wrote: > here it is. thanks, > > > > > To: freesurfer@nmr.mgh.harvard.edu > > From: gr...@nmr.mgh.harvard.edu > > Date: Fri, 15 Jan 2016 12:00:02 -0500 > > Subject: Re: [Fre

Re: [Freesurfer] mri_surf2vol {Disarmed}

sure what you are asking about in terms of gray matter. On 01/15/2016 12:27 PM, Xiaomin Yue wrote: > The voxel size is 1.5mm. Some of voxels in the gray matter are not > included in the mask as well. Why? > > Xiaomin > > > > > On Fri, Jan 15, 2016 at 9:21 AM

Re: [Freesurfer] mri_surf2vol {Disarmed}

Thanks. Xiaomin On Fri, Jan 15, 2016 at 11:41 AM -0800, "Douglas N Greve" wrote: or you can add --fillribbon to your surf2vol command (but the label2vol method is probably better) On 01/15/2016 12:32 PM, Xiaomin Yue wrote: > Maybe, I misunderstand it. Is the pial surface

Re: [Freesurfer] temporal lobe pial surface problem

images. Do you have contrast in the temporal lobe? Frequently it goes away at 7T due to dielectric effects. I'll cc Jon Polimeni who is our 7T (among other things!) expert. cheers Bruce On Fri, 15 Apr 2016, Xiaomin Yue wrote: > Hi Bruce, > I have done the recon-all (fs5.3) with th

Re: [Freesurfer] temporal lobe pial surface problem

5 Apr 2016, Xiaomin Yue wrote: > Hi Bruce, > I have done the recon-all (fs5.3) with the data collected from a 7T scanner > using MP2Rage. The recon went well without problem. But the the temporal > reconstruction looks clearly not correct (see attached). I tried to push > th

Re: [Freesurfer] temporal lobe pial surface problem

x27;s tough to make out much from the snapshots, if you upload the entire subject dir to our ftp site I'll take a lookCheersBruce On Apr 18, 2016, at 7:13 PM, Xiaomin Yue wrote: Hi Jon, Thanks for your answers. There is gray-white contrast in the temporal lobe, but same as you said that th

Re: [Freesurfer] temporal lobe pial surface problem

____________ > > Von: freesurfer-boun...@nmr.mgh.harvard.edu > > [freesurfer-boun...@nmr.mgh.harvard.edu]" im Auftrag von "Xiaomin Yue > > [yu...@hotmail.com] > > Gesendet: Dienstag, 19. April 2016 01:13 &g

Re: [Freesurfer] temporal lobe pial surface problem

matter. 70 is way too low On Tue, 19 Apr 2016, Xiaomin Yue wrote: > The white matter in the anterior temporal lobe is around 70, the gray matter > is about 30. The number is read from brain.finalsurfs.mgz. > Xiaomin > > > Date: Tue, 19 Apr 2016 09:29:50 -0400 > > From: fi

[Freesurfer] Basename error

scussion thread in the above link. Any suggestions? Thanks, Xiaomin Yue ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e

Re: [Freesurfer] Basename error

ect: Re: [Freesurfer] Basename error what is your command line and terminal output On 6/19/14 4:36 PM, Xiaomin Yue wrote: Hi all, I am analyzing functional data using fsfast 5.3 with the

Re: [Freesurfer] Basename error

r it may fail. Try putting > $FREESURFER_HOME/fsfast/toolbox first in your matlab path > > > On 06/22/2014 02:52 PM, Xiaomin Yue wrote: > > Hi Doug > > > > Thanks for you response. The command line is: selxavg3-sess -s > > subject_0101 -d . -analysis DoD_loom

[Freesurfer] wm.mgz

Hi, My edited wm.mgz was saved as wm.edited.mgz, then it copied to wm.mgz. I re-run the anlysis using recon-all -s cologna -autorecon2-wm. From some reason, the analysis regenerated wm.mgz from brain.mgz, which of course replaced my edited wm.mgz. Did I do some wrong here? Thanks,Xiaomin

Re: [Freesurfer] wm.mgz

d the file. Have you checked? Bruce On Fri, 25 Jul 2014, Xiaomin Yue wrote: > Hi, > > My edited wm.mgz was saved as wm.edited.mgz, then it copied to wm.mgz. I > re-run the anlysis using > recon-all -s cologna -autorecon2-wm. From some reason, the analysis > regenerated wm

Re: [Freesurfer] wm.mgz

rvard.edu> Subject: Re: [Freesurfer] wm.mgz What version? Check the voxels you erased and see if they were set to 1 instead of 0 > On Jul 25, 2014, at 8:39 PM, Xiaomin Yue wrote: > > Hi Bruce, > > Thanks for your response. the editing was done in freeview. I saved the > e

Re: [Freesurfer] wm.mgz

erved unless they are 1 > On Jul 25, 2014, at 9:33 PM, Xiaomin Yue wrote: > > It is 5.3. The voxels erased was set as 0. Is that the problem? If so, I > can try to replace 0 with 1. > > Xiaomin > From: Bruce Fischl > Sent: ‎7/‎25/‎2014 9:22 PM > To: Freesurfer sup

Re: [Freesurfer] missing anterior temporal lobe

Hi, I had successfully reconstructed a primate brain using fs5.3. But one part of left anterior temporal lobe was not correct, even with the accurate wm.mgz. See attached image for what I mean. Are there parameters to be used to correct this problem? Thanks,Xiaomin

Re: [Freesurfer] NIH Staff Scientist Position available, Bethesda, MD, USA

The title has been FedEx for overnight. Please let me know after getting it. Xiaomin From: Thomas, Adam (NIH/NIMH) [E] Sent: ‎7/‎30/‎2014 6:36 AM To: freesurfer@nmr.mgh.harvard.edu; FSL - FMRIB's Softwa

[Freesurfer] volume to surface registration problem

. Attached is the registration log file. Any suggestions will be appreciated. Xiaomin Yue Logfile for bbregister Thu Oct 16 10:54:36 EDT 2014 setenv SUBJECTS_DIR /misc/data41/yuex/human_anat cd /misc/data41/yuex/humanfMRI/human_curvature/subjdata/field090514

Re: [Freesurfer] volume to surface registration problem

t; cd /misc/data41/yuex/humanfMRI/human_curvature/subjdata/field090514 > bbregister --s field --init-spm --6 --bold --mov bold/template.nii --reg > bold/register.dof6.dat --init-reg-out bold/init.register.dof6.dat > > > > > On 10/16/2014 11:14 AM, Xiaomin Yue wrote: > >

Re: [Freesurfer] volume to surface registration problem

rom > register-sess. > > On 10/16/2014 12:04 PM, Xiaomin Yue wrote: > > Hi Doug, > > > > Thanks for the promptly response. I do have spm8 and spm12b > > installed. Which version should I use? Also, how to change the spm > > as the inital registration met

[Freesurfer] thickness from pial and white

Hi All, Cortical surface reconstructed using caret from a high resolution MRI data (0.25 mm) has been converted to freesurfer format, and viewed correctly using freeview. My questions are whether it is possible to generate 1) a ?h.thickness from the ?h.pial and ?h.white; 2) wm

Re: [Freesurfer] thickness from pial and white

urfer] thickness from pial and white the thickness you can generate using mris_thikness. Why do you want to generate a wm.mgz? I guess you could from the wmparc On Mon, 8 Dec 2014, Xiaomin Yue wrote: > > Hi All, > > > > Cortical surface reconstructed using caret from a high reso

Re: [Freesurfer] thickness from pial and white

What I mean by inputs is the default files the mris_thickness will be looking for to run correctly Xiaomin > On Dec 9, 2014, at 1:08 PM, Xiaomin Yue wrote: > > Hi Bruce, > > Thanks for your response. What's the inputs to the mris_thickness? I need > the wm.mgz t

Re: [Freesurfer] thickness from pial and white

Thanks very much. Does this create curvature file? Again, is it possible to generate wm.mgz from those files? Thanks, Xiaomin > On Dec 9, 2014, at 4:19 PM, Bruce Fischl wrote: > > I think just the ?h.white and ?h.pial > > cheers > Bruce >> On Tue, 9 Dec

Re: [Freesurfer] thickness from pial and white

erate. You could use mris_fill to generate the interior of the ?h.white surface, then use the aseg to remove non-wm voxels I guess On Tue, 9 Dec 2014, Xiaomin Yue wrote: > Thanks very much. Does this create curvature file? Again, is it possible to > generate wm.mgz from those files?

Re: [Freesurfer] thickness from pial and white

erate the interior of the ?h.white surface, then use the aseg to remove non-wm voxels I guess On Tue, 9 Dec 2014, Xiaomin Yue wrote: > Thanks very much. Does this create curvature file? Again, is it possible to > generate wm.mgz from those files? > > Thanks, > Xiaomi

Re: [Freesurfer] thickness from pial and white

Yes, lh.pial exists Xiaomin > On Dec 10, 2014, at 10:33 AM, Bruce Fischl wrote: > > it only looks for that if it can't find lh.pial. Does that exist? > >> On Wed, 10 Dec 2014, Xiaomin Yue wrote: >> >> Hi Bruce, >> the mris_thickness was looking f

Re: [Freesurfer] thickness from pial and white

Yes, lh.pial exists Xiaomin > On Dec 10, 2014, at 10:33 AM, Bruce Fischl wrote: > > it only looks for that if it can't find lh.pial. Does that exist? > >> On Wed, 10 Dec 2014, Xiaomin Yue wrote: >> >> Hi Bruce, >> the mris_thickness was looking f

Re: [Freesurfer] thickness from pial and white

pial and white what version of FS do you have? You can try runing it with -pial pial but I wouldn't think that is needed. Is the lh.pial in /misc/data41/yuex/recon_test/test_DB48/surf/ and is it readable? On Wed, 10 Dec 2014, Xiaomin Yue wrote: > Yes, lh.pial exists > > Xiaom

[Freesurfer] freeview 3.0

External Email - Use Caution Dear all, The Freeview (3.0) coming with fs 7.1 can not show any surface brain (inflated, pial, white) in a solid color. The Freeview is currently running under WSL and was running without a problem until I updated libXm4. Is there a particular li

Re: [Freesurfer] freeview 3.0

n your system that installed Motif and/or also maybe changed the X windows distribution libraries (as used by freeview). - R. On Jul 9, 2020, at 12:54, Xiaomin Yue wrote: External Email - Use Caution Hi, Here is the command I used in the freeview 3.0: freeview – f $SUBJE

Re: [Freesurfer] freeview 3.0

le libraries or graphics card driver. Ruopeng On Jul 9, 2020, at 10:38 PM, Xiaomin Yue mailto:yu...@hotmail.com>> wrote: External Email - Use Caution Thanks for your response. Why does freeview 2 work? Thanks, Xiaomin From: fsbuild<mailto:fsbu...@contbay.com> Sent: Thursda

[Freesurfer] mri_fieldsign error

External Email - Use Caution Hi Doug, I used FS 7.1 under WSL to analyze retinotopy data. Since the ring and wedge were presented at a different frequency, the data had to be analyzed separately for each condition. To get the field sign, I had to use the mri_fieldsign functio

Re: [Freesurfer] mri_fieldsign error

External Email - Use Caution Hi All, Just in case the below poster was missed. Thanks, Xiaomin From: Xiaomin Yue<mailto:yu...@hotmail.com> Sent: Saturday, July 11, 2020 1:43 PM To: Freesurfer support list<mailto:freesurfer@nmr.mgh.harvard.edu> Subject:

Re: [Freesurfer] mri_fieldsign error

.edu It will ask you for a user name: use "anonymous" (no quotes) It will ask you for a password: use "anonymous" (no quotes) cd transfer/incoming binary put subject.tar.gz Send an email that the file has been and the name of the file. On 7/15/2020 11:07 AM, Xiaomin Yue wrote:

Re: [Freesurfer] mri_fieldsign error

External Email - Use Caution Yes. I will try it on a real Linux box and let you know. Thanks, Xiaomin From: Douglas N. Greve<mailto:dgr...@mgh.harvard.edu> Sent: Friday, July 17, 2020 5:32 PM To: Xiaomin Yue<mailto:yu...@hotmail.com>; Freesurfer support list<ma

Re: [Freesurfer] mri_fieldsign error

External Email - Use Caution I tried on our Linux: Centos Linux 7 (core), ID_like = ‘rhel fedora’ with the same “segmentation fault (core dumped)” error. Thanks, Xiaomin From: Xiaomin Yue<mailto:yu...@hotmail.com> Sent: Friday, July 17, 2020 6:07 PM To: Freesurfer suppor