Re: [Freesurfer] missing 3volreg.afni

Hi Douglas, It still does not work. 2015-12-21 23:29 GMT+07:00 Douglas N Greve : > that link works for me. Can you try again? > > On 12/20/2015 02:17 AM, Thục Trinh wrote: > > Hi FS experts, > > > > I'm working on my fMRI data using FSFAST v.6 tool. But the first step > > of Preproc-sess was fail

Re: [Freesurfer] missing 3volreg.afni

what happens when you click on it? On 12/22/15 9:28 AM, Thục Trinh wrote: Hi Douglas, It still does not work. 2015-12-21 23:29 GMT+07:00 Douglas N Greve >: that link works for me. Can you try again? On 12/20/2015 02:17 AM, Thục Trinh wrote: > Hi

[Freesurfer] FW: problem with hard coded directory (/scratch)

Hi Bruce, I reported the error related to '/scratch' a couple of weeks ago. We just tested the newest version of freesurfer 6.0. It looks likes that a lot of "if (-e /scratch)" have been changed to "if (-dw /scratch)". However, there are still a lot of binaries in the bin directory that match

Re: [Freesurfer] FW: problem with hard coded directory (/scratch)

what do you mean "match the string scratch"? Can you point us to a problematic binary? On 12/22/15 11:28 AM, Fengji Geng wrote: Hi Bruce, I reported the error related to '/scratch' a couple of weeks ago. We just tested the newest version of freesurfer 6.0. It looks likes that a lot of "if (

[Freesurfer] variable TR

Hi Surfers We are wondering if we can use freesurfer to analyze ECG-gated fmri. As far as I see, mkanalysis-sess expects a fix TR. Since we are in the design stage, any hint or suggestion to facilitate future data analysis will be highly appreciated. Regards

Re: [Freesurfer] Trac-all -path Segmentation error

Hi Katherine - Have you looked at any of the intermediate images? Do they look normal? a.y On Mon, 21 Dec 2015, Katherine Damme wrote: > Hello Everyone! > > It looks as though my prep and bedp stages completed properly, but the prep > stage ends in a segmentation > errror. > > See attached

Re: [Freesurfer] variable TR

No, you need to simultaneously estimate the T1. Mike Harms did this years ago. On 12/22/15 11:37 AM, sha...@nmr.mgh.harvard.edu wrote: > Hi Surfers > We are wondering if we can use freesurfer to analyze ECG-gated fmri. As > far as I see, mkanalysis-sess expects a fix TR. Since we are in the >

[Freesurfer] Mind Research Network - Postdoctoral Fellow

*Mind Research Network* *Postdoctoral Fellow – Job # 2015.180.M* *Summary* A post-doctoral research position is currently available in Dr. Andrew Mayer’s laboratory at The Mind Research Network, Albuquerque, New Mexico location in the area of cognitive neuroscience. The candidate will work on se

[Freesurfer] Virtual machine (in virtual box) generating error: Can't locate MNI/Startup.pm in @INC

Hello freesurfers, I installed freesurfer in a linux machine without problems, but when I am trying to install it on a Windows computer within a virtualmachine I keep getting the same error. I’ve tried the instructions in the tutorial and also tried to set an entirely new virtual machine with the

Re: [Freesurfer] Recon-all: Pial surface error in cingulate region

Hi Jaiashre hmmm, that looks like something we fixed a while ago. What version are you running? cheers Bruce On Tue, 22 Dec 2015, Jaiashre Sridhar wrote: Hello, I am trying to manually edit and fix an error that is occurring in the longitudinal time point of a subject. The error is on the ri

Re: [Freesurfer] lGI value is aberrantly high

Dear all, I have a problem with the LGI module. At the step when the software computes the LGIs for the vertices, In one vertex the lGI results aberrantly high and the software exits with ERRORS. I tried the solution suggested by Marie Schaer to rereconstruct The images with "randomness" Recon-al

Re: [Freesurfer] Recon-all: Pial surface error in cingulate region

Dr. Fischl, I am using FS version 5.1.0 Thanks, Jaiashre. ___ 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 who

Re: [Freesurfer] missing 3volreg.afni

The link is fine. But when I click on the 3dvolreg file to get the download, it failed with the error: "this webpage is not available" 2015-12-22 23:12 GMT+07:00 Douglas Greve : > what happens when you click on it? > > > On 12/22/15 9:28 AM, Thục Trinh wrote: > > Hi Douglas, > It still does not w

Re: [Freesurfer] missing 3volreg.afni

Try this one ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/3dvolreg.afni On 12/22/15 7:56 PM, Thục Trinh wrote: The link is fine. But when I click on the 3dvolreg file to get the download, it failed with the error: "this webpage is not available" 2015-12-22 23:12 GMT+07:00 Doug

Re: [Freesurfer] Recon-all: Pial surface error in cingulate region

I see. That's quite old, which I think is why you are having this problem. I'm not sure if it was fixed in 5.3 or not, but definitely not in 5.1. Can you try 5.3? On Tue, 22 Dec 2015, Jaiashre Sridhar wrote: Dr. Fischl, I am using FS version 5.1.0 Thanks, Jaiashre.  _

Re: [Freesurfer] Recon-all: Pial surface error in cingulate region

Dr. Fischl, Since it is a longitudinal study, we have to stick to using 5.1 version. Thanks, Jaiashre. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e

Re: [Freesurfer] Recon-all: Pial surface error in cingulate region

Why? YOu could reprocess all the data with 5.3 (which has a *much* better longitudinal stream than 5.1) On Wed, 23 Dec 2015, Jaiashre Sridhar wrote: Dr. Fischl, Since it is a longitudinal study, we have to stick to using 5.1 version. Thanks, Jaiashre.  __

[Freesurfer] recon-all error

Hi Freesurfers, I am currently learning how to use freesurfer to process the brain image and I acknowledge your great job. I contacting you regarding that I got an error after using recon-all command. By the way i am sill beginner in both linux and freesurer. Here is the log of the error abdol

Re: [Freesurfer] recon-all error

Hi Abdulqaw You need to specify an input T1-weighted volume, either explicitly with -i , or implicitly by converting the volume you want to process into mgz format and naming it 001.mgz and placing it in the orig sub directory. Cheers Bruce > On Dec 22, 2015, at 10:27 PM, abdulkawi alareefi ala

Re: [Freesurfer] recon-all error

It could not find any data. It is looking for something like $SUBJECTS_DIR/mine/mri/orig/001.mgz. Alternatively, you can run recon-all with -i and pass the input. On 12/22/15 10:27 PM, abdulkawi alareefi alareefi wrote: Hi Freesurfers, I am currently learning how to use freesurfer to process t

Re: [Freesurfer] missing 3volreg.afni

Hi, It comes up with this error: /freesurfer/bin/3dvolreg.afni: Exec format error. Wrong Architecture. ERROR: 3dvolreg.afni Invalid null command. 2015-12-23 7:59 GMT+07:00 Douglas Greve : > Try this one > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/3dvolreg.afni > > On 12/22/15