Re: [Freesurfer] preproc-sess (AP-PA) - study design

fsfast does not work with topup in this way. You can do a couple of things (1) do the preprocessing yourself and then turn it off for fsfast (2) create your own B0 map and put it in to sessid/fsd/b0dcmap.nii.gz   and specify -b0dc in mkanalysis-sess On 12/8/2022 9:50 AM, Asa Borzabadi Farahan

Re: [Freesurfer] Preproc-sess crashed - 3dvolreg.afni error

External Email - Use Caution On MacOS I would try running the fs_install_mcr script with, $ export FREESURFER_HOME=/Applications/freesurfer/7.3.2 $ source $FREESURFER_HOME/SetUpFreeSurfer.sh <... output showing SUBJECTS_DIR and other environment variables> $ cd  $FREESURFER_HOM

Re: [Freesurfer] Preproc-sess crashed - 3dvolreg.afni error

External Email - Use Caution Preproc worked -- it seems it was an issue in setting up my freesurfer set up file! I am now running into an error with FSFAST functions that require MATLAB. I downloaded MATLAB runtime using the command in freesurfer (fs_install_mcr R2014b) which dow

Re: [Freesurfer] Preproc-sess crashed - 3dvolreg.afni error

is it in $FREESURFER/bin ? If so, is that folder in your path? On 10/27/2022 12:49 PM, Gillian Grennan wrote: External Email - Use Caution Realized I sent this to the support list not back to you! But it says "command not found" when I run 3dvolreg and 3dvolreg.afni On Wed, Oct 26,

Re: [Freesurfer] Preproc-sess crashed - 3dvolreg.afni error

External Email - Use Caution Realized I sent this to the support list not back to you! But it says "command not found" when I run 3dvolreg and 3dvolreg.afni On Wed, Oct 26, 2022 at 7:24 AM Douglas N. Greve wrote: > What happens when your run 3dvolreg.afni by itself (no options)

Re: [Freesurfer] Preproc-sess crashed - 3dvolreg.afni error

External Email - Use Caution It says "command not found" (when I run 3dvolreg and 3dvolreg.afni)! On Wed, Oct 26, 2022 at 7:24 AM Douglas N. Greve wrote: > What happens when your run 3dvolreg.afni by itself (no options) from the > command line? > > On 10/25/2022 4:41 PM, Gillia

Re: [Freesurfer] Preproc-sess crashed - 3dvolreg.afni error

What  happens when your run 3dvolreg.afni by itself (no options) from the command line? On 10/25/2022 4:41 PM, Gillian Grennan wrote: External Email - Use Caution Hello FreeSurfer Developers, I downloaded Freesurfer v7.3.2

Re: [Freesurfer] preproc-sess output

You'll have to load it as an overlay to a surface, eg, freeview -f $FREESURFER_HOME/subjects/fsaverage/surf/lh.inflated:overlay=fmcpr.up.sm5.fsaverage.lh.nii.gz there won't be much to see :) On 9/8/2021 5:51 AM, Alice Giubergia wrote: External Email - Use Caution Dear Freesurfer's e

Re: [Freesurfer] preproc-sess fmri image to self surface

External Email - Use Caution The command I used is in load_untouch_nii.png and the dimension shown in this file is in the dimension.png. It seems that the dimension used matlab command is 1*1*1*120. Thank you Mingyang Xia On Thu, May 27, 2021 at 3:00 PM Douglas N. Greve wrote: >

Re: [Freesurfer] preproc-sess fmri image to self surface

you'll need to supply us with more information, eg, command lines and  why do you think it has the wrong dimensions On 5/25/2021 11:53 PM, Mingyang Xia wrote: External Email - Use Caution Dear freesurfer expert:   My name is Mingyang. I want to preprocess fmri image and map the timep

Re: [Freesurfer] preproc-sess error with FreeSurfer 7.1

Thursday, October 29, 2020 9:33 PMTo: freesur...@nmr.mgh.harvard.eduCc: Peled, Noam <npe...@mgh.harvard.edu>Subject: Re: [Freesurfer] preproc-sess error with FreeSurfer 7.1 External Email - Use CautionHello Noam, The python script /usr/local/freesurfer/dev/bin/slicedelay n

Re: [Freesurfer] preproc-sess error with FreeSurfer 7.1

October 29, 2020 9:33 PM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Cc: Peled, Noam mailto:npe...@mgh.harvard.edu>> Subject: Re: [Freesurfer] preproc-sess error with FreeSurfer 7.1 External Email - Use Caution Hello Noam, The python script

Re: [Freesurfer] preproc-sess error with FreeSurfer 7.1

pe...@mgh.harvard.edu>Subject: Re: [Freesurfer] preproc-sess error with FreeSurfer 7.1 External Email - Use CautionHello Noam, The python script /usr/local/freesurfer/dev/bin/slicedelay needs to be run with a version of python that is 2.X, i.e., $ file /usr/local/freesurfe

Re: [Freesurfer] preproc-sess error with FreeSurfer 7.1

-rwxrwxr-x 1 rd521 rd521 4951 Oct 30 04:45 /usr/local/freesurfer/dev/bin/slicedelay Thanks! From: Greve, Douglas N.,Ph.D. Sent: Friday, October 30, 2020 10:38 AM To: Peled, Noam ; Freesurfer support list Cc: Gumenyuk, Valentina ; Stufflebeam, Steven M. ; Douglas N Greve Subject: Re: preproc

Re: [Freesurfer] preproc-sess error with FreeSurfer 7.1

can you send the result of ls -l `which  slicedelay` On 10/29/2020 8:47 PM, Peled, Noam wrote: Dear FreeSurfer experts! We are running FsFast pipeline to analysis our language task for epilepsy patients. Usually we are using FreeSurfer 5.3. We want to use a newer version, so I decided to

Re: [Freesurfer] preproc-sess error with FreeSurfer 7.1

@nmr.mgh.harvard.edu Cc: Peled, Noam Subject: Re: [Freesurfer] preproc-sess error with FreeSurfer 7.1 External Email - Use Caution Hello Noam, The python script /usr/local/freesurfer/dev/bin/slicedelay needs to be run with a version of python that is 2.X, i.e., $ file /usr/local/freesurfer/dev

Re: [Freesurfer] preproc-sess error with FreeSurfer 7.1

External Email - Use Caution Hello Noam, The python script /usr/local/freesurfer/dev/bin/slicedelay needs to be run with a version of python that is 2.X, i.e., $ file /usr/local/freesurfer/dev/bin/slicedelay/usr/local/freesurfer/dev/bin/slicedelay: Python script, ASCII text exec

Re: [Freesurfer] preproc-sess - motion correction problem

I'm guessing that AFNI can't do MC on a 2d "volume" (MC is inherently a 3D operation). You can try turning off MC in preproc-sess with -nomc On 9/25/2020 11:56 AM, Nasr, Shahin,Ph.D. wrote: Hi Surfers,      I have faced an issue with preproc-sess and I appreciate your help.  I have a single s

Re: [Freesurfer] preproc-sess mask issue

wishes, > Kevin > Date: Tue, 15 Jan 2019 21:47:37 +0000 From: "Greve, Douglas N.,Ph.D." > Subject: Re: [Freesurfer] preproc-sess mask > issue To: "freesurfer@nmr.mgh.harvard.edu" > Message-ID: > <5b4ea669-5ade-6be4-2435-aed05faf1...@mgh.harvard.edu> C

Re: [Freesurfer] preproc-sess mask issue

? Thank you again for your help! Best wishes, Kevin Date: Tue, 15 Jan 2019 21:47:37 + From: "Greve, Douglas N.,Ph.D." Subject: Re: [Freesurfer] preproc-sess mask issue To: "freesurfer@nmr.mgh.harvard.edu" Message-ID: <5b4ea669-5ade-6be4-2435-aed05faf1...@mgh.harvard.

Re: [Freesurfer] preproc-sess mask issue

Yea, the 5.3 stream used FSL brain masking to make the masks for the fmri. Version 6 uses the FS brain mask transferred into fmri space. Inevitably, you will have to do a lot of reprocessing. The simplest thing to do is to delete the mask files in session/bold/masks and sessoin/bold/RRR/masks (

Re: [Freesurfer] preproc-sess with symbolic links

Why do you think this has to do with sym links? Can you run the preproc-sess command with -debug as the first option and send the results? On 11/08/2017 11:50 AM, Tuominen, Lauri Johannes wrote: > Hi all, > I’m trying to run preproc-sess using symbolic links in my SUBJECTS_DIR but > the program

Re: [Freesurfer] Preproc-sess Error

way to get this done? Thanks so much for the help! > > --Eugene > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu > on behalf of Douglas Greve > > *Sent:* Wednesday, October 25, 2017 5:39:27 PM > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* Re: [Freesurfer] Prepro

Re: [Freesurfer] Preproc-sess Error

arvard.edu Subject: Re: [Freesurfer] Preproc-sess Error it is not in $FREESURFER_HOME/bin ? If not, you can copy it from 5.3 On 10/25/17 4:59 PM, Hsu, Eugene wrote: Hi FreeSurfer Experts, We're trying to run preproc-sess on FreeSurfer 6, but we're encountering an error when motion cor

Re: [Freesurfer] Preproc-sess Error

it is not in $FREESURFER_HOME/bin ? If not, you can copy it from 5.3 On 10/25/17 4:59 PM, Hsu, Eugene wrote: Hi FreeSurfer Experts, We're trying to run preproc-sess on FreeSurfer 6, but we're encountering an error when motion correcting:     ERROR: cannot find AFNI command 3dvolreg.afni

Re: [Freesurfer] preproc-sess

Technically, it does not use an anatomical volume but rather the surfaces derived from the conformed volume (so the registration will be good for any conformed volume). No need to reorient the functionals as long as the header info about the head orientation is correct. On 10/6/17 5:29 PM, Ji

Re: [Freesurfer] preproc-sess

Thanks Bruce and Doug! Follow-up questions: which anatomical volume does bbregister register the functional to? Also, is there any need to reorient the functional image before preprocessing? On Tue, Sep 5, 2017 at 11:34 AM, Douglas N Greve wrote: > > > On 08/31/2017 11:47 AM, Jiahe Zhang wrote:

Re: [Freesurfer] preproc-sess

On 08/31/2017 11:47 AM, Jiahe Zhang wrote: > Dear Freesurfer experts, > > I have two questions regarding preproc-sess: > > 1) What is the default algorithm that does the functional-anatomical > registration? And is there any way to change the default to other > types of registration methods? it

Re: [Freesurfer] preproc-sess

1) bbregister ("Accurate and robust brain image alignment using...") 2) We don't typically resample - most analyses are done in native space by default cheers Bruce On Thu, 31 Aug 2017, Jiahe Zhang wrote: > Dear Freesurfer experts, > I have two questions regarding preproc-sess: > > 1) What is

Re: [Freesurfer] preproc-sess -per-run vs. -per-session

Thanks for the reply, Doug! Best, Feilong On Wed, Mar 22, 2017 at 1:24 PM, Douglas Greve wrote: > I think the motion correction works a little better if done to a reference > inside each run, and there's probably less interpolation in the end > > On 3/20/17 11:04 AM, Feilong Ma wrote: > > Hi Fr

Re: [Freesurfer] preproc-sess -per-run vs. -per-session

I think the motion correction works a little better if done to a reference inside each run, and there's probably less interpolation in the end On 3/20/17 11:04 AM, Feilong Ma wrote: Hi FreeSurfer Experts, I was reading the document of preproc-sess, and it seems -per-run is recommended inste

Re: [Freesurfer] preproc-sess - Cannot allocate memory

what is your command line? Also, please send the entire terminal output On 03/03/2017 01:52 PM, Peled, Noam wrote: > Hey all, > I'm running preproc-sess, and getting the following error: > ... > Reading in mov rest/tmp.bbregister.28405/template.nii > Reading in ref .../mri/brainmask.mgz > Reading

Re: [Freesurfer] preproc-sess brain masks in masks subdirectory

There should be, but if everything is running properly, then it is not a problem. If the masks are needed and are not there, then the processing will die. On 01/02/2017 01:47 PM, Ladan Shahshahani wrote: > Dear experts, > Hi, > > I ran the preproc-sess command. I was following the tutorial page

Re: [Freesurfer] preproc-sess error opening tmp brain_mask

both computers point to the same place, and I > can run something like fslview on both computers. > > From: Douglas N Greve > Sent: Friday, April 22, 2016 1:54 PM > To: Mcnorgan, Christopher > Subject: Re: [Freesurfer] preproc-sess error o

Re: [Freesurfer] preproc-sess error opening tmp brain_mask

Can you run /mkbrainmask-sess//-debug -s FS_T1_501 //-fsd bold/ |& tee dng.log and send me dng.log ? doug On 04/18/2016 04:51 PM, Mcnorgan, Christopher wrote: > du -h /tmp/ shows 256GB available, so that doesn’t seem to be it. Is > the “not found” error telling me that a binary is not found,

Re: [Freesurfer] preproc-sess error opening tmp brain_mask

du -h /tmp/ shows 256GB available, so that doesn’t seem to be it. Is the “not found” error telling me that a binary is not found, or that some expected output file is not found? I was looking for /bin/imtest and /bin/remove_ext, and those binaries indeed do not exist, but we’ve run Freesurfer on

Re: [Freesurfer] preproc-sess error opening tmp brain_mask

Is your /tmp space full? On 04/15/2016 12:54 PM, Mcnorgan, Christopher wrote: > > I was hoping the developers might be able to help with a problem I'm > having with a sub-step of preproc-sess. > > > I executed the following: > > preproc-sess -s FS_T1_501 -surface self lhrh -fwhm 6 -per-run -fsd b

Re: [Freesurfer] preproc-sess and stc question

Hi Chaz, unfortunately version 5 does not support arbitrary slice orders. It will be available in version 6. doug On 11/03/2015 06:27 PM, Gay,Charles Wysaw wrote: > Hi - > > 1) I am trying to perform preprocessing steps on functional task data > that was acquired on a Phillips scanner using an i

Re: [Freesurfer] Preproc-sess failed

Yay !!! It works finally. So the problem in the first place is: I got the wrong version of shared library :) Thank you so much. 2015-07-01 14:58 GMT+07:00 Jalmar Teeuw : > Yes, the sudo prefix is optional, but may be required otherwise you get a > 'not authorized' message (i.e. you need administ

Re: [Freesurfer] Preproc-sess failed

Is the command line like this: yum install libXp.so.6.x86_64 because I did run yum install libXp.so.6 before and it did not work. 2015-07-01 11:28 GMT+07:00 Z K : > Yes, and when it is done installing, determine exactly what directory the > libXp.so.6 file was installed into. That is the directo

Re: [Freesurfer] Preproc-sess failed

Yes, and when it is done installing, determine exactly what directory the libXp.so.6 file was installed into. That is the directory you want to add to your LD_LIBRARY_PATH environment variable. -Zeke > On Jun 30, 2015, at 11:39 PM, Thục Trinh wrote: > > Hi, > I did exactly what you said, a

Re: [Freesurfer] Preproc-sess failed

Hi, I did exactly what you said, and the error still remain: *3dvolreg.afni: error while loading shared libraries: libXp.so.6: cannot open shared object file: No such file or directory* I cannot find any folder name libXp.so.6,should I re-download libXp.so.6 64 bits ? 2015-06-29 18:15 GMT+07:00 J

Re: [Freesurfer] Preproc-sess failed

Sorry, I didn't have access to my CentOS machine, the 32-bit libraries use the suffix i686 instead of i386, so try   sudo yum remove libXp.i686 By removing the 32-bit version you essential ensure only the 64-bit version is available when the application tries to load libXp. Hope that works. My

Re: [Freesurfer] Preproc-sess failed

Hi, "yum remove libXp.i386" command returns with *No Packages marked for removal* This is my output for:'file $FREESURFER_HOME/bin/3dvolreg.afni' */usr/local/freesurfer/bin/3dvolreg.afni: ELF 64-bit LSB executable, x86-64, version 1 (GNU/Linux), statically linked, stripped* 2015-06-26 16:19 GMT+0

Re: [Freesurfer] Preproc-sess failed

Have you tried removing the 32-bit version of the libraries? I believe it is yum remove libXp.i386 What is the output of file $FREESURFER_HOME/bin/3dvolreg.afni Maybe you could try locate all the libXp.so on your system and see if there is a local 32-bit copy find / -type f -iname "li

Re: [Freesurfer] Preproc-sess failed

the lib files are now in /usr/lib64, the ERROR still the same after I set a new path for shared lib with this command in .bashrc file *export LD_LIBRARY_PATH=/usr/lib64:$LD_LIBRARY_PATH* the Error still the same. *3dvolreg.afni: error while loading shared libraries: libXp.so.6: wrong ELF class: ELF

Re: [Freesurfer] Preproc-sess failed

Is still gives you the same error? I'm not certain about libXpm; I recall having to install certain libraries on a slimmed down version of Centos 6.5, libXp and libXpm were amongst those libraries. For me, the lib files are stored in /usr/lib64 Try find /usr/lib64 -type f -iname "libXp*" -p

Re: [Freesurfer] Preproc-sess failed

Hi, After complete install the suitable version of shared library as you suggested, I cannot find any file name libXpm.x86_64 to set the new path for shared library. Ps: Is there any differences between libXpm.x86_64 and libXp.x86_64 2015-06-24 16:03 GMT+07:00 Jalmar Teeuw : > That sounds more li

Re: [Freesurfer] Preproc-sess failed

That sounds more like you have only the 32-bit version of the libXp installed when 64-bit is required. Are you using the 64-bit version of Freesurfer 5.3.0 for CentOS 6 that is available on the downloads page? Have you tried sudo yum install libXp.x86_64 on the terminal? This should install

Re: [Freesurfer] Preproc-sess failed

I did that, and run the command 3dvolreg.afni on Terminal to check. The Error still remain: *3dvolreg.afni: error while loading shared libraries: libXp.so.6: wrong ELF class: ELFCLASS32* 2015-06-23 10:39 GMT+07:00 Z K : > From reading the email thread history, it appears you may have downloaded >

Re: [Freesurfer] Preproc-sess failed

From reading the email thread history, it appears you may have downloaded the apple OS X version of 3rvolreg.afni and overwrote the original, which is the cause of the error. Please extract the original version of that binary from the original tarball. If you no longer have it you can download i

Re: [Freesurfer] Preproc-sess failed

hello, I am using CentOS release 6.4 ( final) 64bit and Freesurfer v.5.3.0. I think that makes the confliction. 2015-06-23 8:26 GMT+07:00 Thục Trinh : > Hello Douglas and ZK, > I set the path for shared library in my .basrch file, but it still does > not work and comes up with this Error: > *3dvo

Re: [Freesurfer] Preproc-sess failed

Hello Douglas and ZK, I set the path for shared library in my .basrch file, but it still does not work and comes up with this Error: *3dvolreg.afni: error while loading shared libraries: libXp.so.6: wrong ELF class: ELFCLASS32* *ERROR: 3dvolreg.afni* *Invalid null command.* Trinh 2015-06-23 3:03

Re: [Freesurfer] Preproc-sess failed

Trinh, Attempt to determine where libXp.so.6 was installed on your system after you installed it using yum. For example, on my system libXp.so.6 exists in directory "/usr/lib64". Once you determine the location where the library resides, add that directory to your LD_LIBRARY_PATH after you sou

Re: [Freesurfer] Preproc-sess failed

I'm not sure what to tell you. Zeke, do you have any ideas? Alternatively, you can just install afni on your machine. Once you verify that the installation works, copy 3dvolreg from the installation. On 6/21/15 3:55 PM, Thục Trinh wrote: Hello Douglas, I already had *3dvolreg.afni* in */freesu

Re: [Freesurfer] Preproc-sess failed

Hello Douglas, I already had *3dvolreg.afni* in */freesurfer/bin/*, but I still download the new one 3dvolreg.afni and replaced it in /freesurfer/bin. But the Error still remain the same. *3dvolreg.afni: error while loading shared libraries: libXp.so.6: cannot open shared object file: No such file

Re: [Freesurfer] Preproc-sess failed

See this thread http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg37764.html On 6/17/15 5:59 PM, Thục Trinh wrote: Hi freesurfer experts, I am practicing on the fsfast tutorial data that were given at Freesurfer website. I run the command to do the pre-processing on the sess01

Re: [Freesurfer] preproc-sess creates files

I'll need more information before I can help you. Please review our bug reporting page to see what kind of info is needed: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting On 06/11/2015 02:44 PM, Park, Jung Mi wrote: > Hello Freesurfer team > > When I ran preprc-sess of dementia patient's fmri, f

Re: [Freesurfer] Preproc-sess failed

that means that the version of 3dvolreg.afni does not match your operating system. What is your OS and what version of FS are you running? On 5/18/15 4:11 AM, Thục Trinh wrote: Hi freesurfer experts, I am practicing on the fsfast tutorial data that were given at Freesurfer website. I run the

Re: [Freesurfer] preproc-sess erros

This is a bug that popped up because the Linux developers changed a shell script behavior in the most recent CentOS. You can get a fix from here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/bbregister doug On 04/02/2013 04:18 PM, Mario Ortega wrote: > Hi freesurfer team, >

Re: [Freesurfer] preproc-sess -surface flag

Use self for retinotopy doug On 03/26/2013 12:24 PM, Y.V. Jiang wrote: > Thanks Doug, this makes sense. What about retinotopic mapping? Should > I use fsaverage or self? > > -Yuhong > > On Tue, Mar 26, 2013 at 10:56 AM, Douglas N Greve > mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > It

Re: [Freesurfer] preproc-sess -surface flag

Thanks Doug, this makes sense. What about retinotopic mapping? Should I use fsaverage or self? -Yuhong On Tue, Mar 26, 2013 at 10:56 AM, Douglas N Greve wrote: > > It should either be fsaverage, or self, or an average subject you have > created. The fMRI analysis is done such that the raw data

Re: [Freesurfer] preproc-sess -surface flag

It should either be fsaverage, or self, or an average subject you have created. The fMRI analysis is done such that the raw data are resampled into the fsaverage space (unless you use self) and processed there in anticipation of doing group analysis. doug On 03/26/2013 10:37 AM, Y.V. Jiang wr

Re: [Freesurfer] preproc-sess

> Hi Doug, > > This is the terminal output. The output volumes don't seem to be smoothed. > > preproc-sess -s 8003 -fsd bold -stc up -fwhm 5 -per-run > -- > preproc-sess logfile is log/preproc-sess.8003.log > -

Re: [Freesurfer] preproc-sess didn't work

yes, you will need FSL. The GUI for mkanalysis was too difficult to maintain so it is nolonger available. doug On 03/07/2013 03:47 AM, 古木 wrote: > Hi,Doug > > When I run"preproc-sess -fsd bold -fwhm 0 -surface self lhrh -sf > sessid -per-run",I met the following problems.Can you tell me why? >

Re: [Freesurfer] preproc-sess

Can you send the terminal output? doug On 03/06/2013 04:33 PM, Meryem Ayse Yucel wrote: > Hi all, > > I am running: > > preproc-sess -s sess01 -fsd bold -fwhm 5 -stc up -per-run > > However at the end it did not create an output like fmcsm. I only have > fmc.nii, fmc.up.nii and fmcpr.up.nii. Am

Re: [Freesurfer] preproc-sess and option -mni305-1mm results in an error

Just subcortical. BTW, going to 1mm will probably create very large files. doug On 11/28/2012 03:52 AM, Jörg Pfannmöller wrote: > A last question to this topic. Does the resolution of the MNI305 brain > affected the surface based analysis or is it exclusively affecting the > subcortical analysis

Re: [Freesurfer] preproc-sess and option -mni305-1mm results in an error

A last question to this topic. Does the resolution of the MNI305 brain affected the surface based analysis or is it exclusively affecting the subcortical analysis? On Tue, 27 Nov 2012 13:30:04 -0500 Douglas N Greve wrote: > Note that each of those set commands should be a single line. The file

Re: [Freesurfer] preproc-sess and option -mni305-1mm results in an error

Note that each of those set commands should be a single line. The file to change is $FREESURFER_HOME/fsfast/bin/rawfunc2tal-sess doug On 11/27/2012 01:23 PM, Douglas N Greve wrote: > Yep, that's a bug. I've fixed it in my version. To fix it in yours, do > the following two steps: > > Step 1: >

Re: [Freesurfer] preproc-sess and option -mni305-1mm results in an error

Yep, that's a bug. I've fixed it in my version. To fix it in yours, do the following two steps: Step 1: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/subcort.mask.1mm.mgz cp subcort.mask.1mm.mgz $SUBJECTS_DIR/fsaverage/mri Step 2: In rawfunc2tal-sess, change: set subcortma

Re: [Freesurfer] preproc-sess

ps, here are slides that explain the masking (along with a bunch of other stuff) http://nmr.mgh.harvard.edu/~greve/fsfast.intro.ppt On 09/24/2012 04:22 PM, Andrew Bock wrote: > Hi Doug, > > I uploaded two example files, as far as I can tell the raw f.nii and > talairach transform look okay. I o

Re: [Freesurfer] preproc-sess

Oh, I see now. There is not a problem here. The volume data has the cortical structure masked out (since those are analyzed in the cortical stream). doug On 09/24/2012 04:22 PM, Andrew Bock wrote: > Hi Doug, > > I uploaded two example files, as far as I can tell the raw f.nii and > talairach tr

Re: [Freesurfer] preproc-sess

Hi Doug, I uploaded two example files, as far as I can tell the raw f.nii and talairach transform look okay. I obtained these files from the tutorial data set, so I'm assuming they were processed properly. Andrew On Mon, Sep 24, 2012 at 1:03 PM, Douglas N Greve wrote: > Actually, before you do

Re: [Freesurfer] preproc-sess

Actually, before you do that, can you check two things 1. Does the raw data (eg, f.nii) look ok? 2. Does the talairach transform for this subject look ok? doug On 09/24/2012 04:02 PM, Douglas N Greve wrote: > Can you upload it to our file drop at > www.nmr.mgh.harvard.edu/facility/filedrop/ > > >

Re: [Freesurfer] preproc-sess

Can you upload it to our file drop at www.nmr.mgh.harvard.edu/facility/filedrop/ On 09/24/2012 02:58 PM, Andrew Bock wrote: > It looks like a very patchy, warped version of the brain. I find that > this is true for all subjects > (/fsfast-functional/sess???/bold/001/fmcpr.up.sm5.mni305.2mm.ni

Re: [Freesurfer] preproc-sess

It looks like a very patchy, warped version of the brain. I find that this is true for all subjects (/fsfast-functional/sess???/bold/001/fmcpr.up.sm5.mni305.2mm.nii.gz). I used both freeview and fslview to visualize the images. On Fri, Sep 21, 2012 at 4:06 PM, Douglas N Greve wrote: > yes, you

Re: [Freesurfer] preproc-sess

yes, you would expect that. what does it look like? how are you visualizing it? On 09/20/2012 06:18 PM, Andrew Bock wrote: > Hello, > > I am attempting to run preproc-sess on my functional data, and am > following the tutorial found here: > http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutoria

Re: [Freesurfer] preproc-sess registration problem

Hi Tapsya, If you want to supply a registration to bbregister, then use --init-reg (and don't use --init-fsl). The xopts should give you the same result as the first command. doug tap...@nmr.mgh.harvard.edu wrote: > Hi Doug, > > As mentioned below (by Dr. Tommi), bbregister with the flag --t1 do

Re: [Freesurfer] preproc-sess registration problem

Hi Doug, As mentioned below (by Dr. Tommi), bbregister with the flag --t1 does provide better results. i.e. >>bbregister --init-fsl --s avml07 --bold --mov bold/template.nii.gz --reg bold/register.dof6.dat --init-reg-out bold/init.register.dof6.dat --t1 However, supplying register.dat (from old

Re: [Freesurfer] preproc-sess registration problem

That should work, but it should not register anyway (unless the raw data or template change). doug r...@nmr.mgh.harvard.edu wrote: > Hi Doug, > > You are absolutely right - I should have noticed the T1 warning in the > bbregister logs. I guess funny things can happen when scanning with a > short

Re: [Freesurfer] preproc-sess registration problem

Hi Doug, You are absolutely right - I should have noticed the T1 warning in the bbregister logs. I guess funny things can happen when scanning with a short (1.15 sec) TR without fat suppression (also this was Trio before the Tim upgrade and multichannel arrays). We tried bbregister with t1 weight

Re: [Freesurfer] preproc-sess registration problem

wow, that's interesting. Your data is actually T1 weighted! There are a couple of things you can do. First, you can copy your register.dat over the register.dof6.dat. An alternative is to run register-sess (bbregister) with t1 weighting. You can do this by creating a file with the line "--t1" i

Re: [Freesurfer] preproc-sess - cannot find AFNI command 3dvolreg

Hi Adam, you'll need to add AFNI into your path (this is a recent change). You can do that in your .cshrc file with something like: setenv AFNIDIR /usr/pubsw/packages/AFNI/current/ set path = ($path $AFNIDIR/bin) doug Adam Nitenson wrote: > Hi Doug and Freesurfers, > > I encountered an err

Re: [Freesurfer] preproc-sess path structure

You should check that anatomical analysis and make sure that it is correct. Once that is done, make sure that the subjectname in the subjectname file is correct, then preproc-sess should run. doug Michelle Umali wrote: > Hi Doug, > > I've run recon-all -all. I ended up inputing an .mgz file co

Re: [Freesurfer] preproc-sess path structure

Hi Doug, I've run recon-all -all. I ended up inputing an .mgz file converted from a .nii file that was converted from a .dicom. Was needed info lost somewhere along the way? Anyway, I thought I ran recon-all -all LD08 (wasn't LD08-anat, does one need -anat?)successfully, because it genera

Re: [Freesurfer] preproc-sess path structure

Hi Michelle, the SUBJECTS_DIR is an environment variable that you have to set prior to running the anatomical analysis (disregarding the functional analysis for a moment). Before running the functional analysis, you must run recon-all on the anatomical data, eg recon-all -all -subject LD08-a

Re: [Freesurfer] preproc-sess

Make sure that your subjectname file has the name of the FreeSurfer subject folder as found in $SUBJECTS_DIR (it looks like it is empty). You don't need the retinotopy data in the $SUBJECTS_DIR. doug Michelle Umali wrote: > Dear Freesurfers, > I am still struggling with the retinotopy analysis.

Re: [Freesurfer] preproc-sess error in version 5.0

OK, I've tracked down and fixed the error. You can get a new version from: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/getrunlist let me know if that works. doug Katherine Sledge Moore wrote: > Hi, > > I was wondering whether there was any progress on this issue (copied > be

Re: [Freesurfer] preproc-sess error in version 5.0

Hi Doug, at /Yukos-iMac:VM/VM00/bold find . -maxdepth 1 -name "[0-9][0-9][0-9]" gave ./001 ./002 ./003 at /Yukos-iMac:VM/VM00/bold/001 find . -maxdepth 1 -name "[0-9][0-9][0-9]" output nothing. Yuko On Thu, Nov 25, 2010 at 4:17 AM, Douglas N Greve wrote: > Yes, that will solve the problem, I

Re: [Freesurfer] preproc-sess error in version 5.0

Yes, that will solve the problem, I just don't know why it's a problem to start with. If you cd into that bold dir, can you run: find . -maxdepth 1 -name "[0-9][0-9][0-9]" doug yuko YY wrote: > Hi Doug, > > "getrunlist /Users/yuko/.../bold" failed, and cd to bold didn't work > either (erro

Re: [Freesurfer] preproc-sess error in version 5.0

Hi Doug, "getrunlist /Users/yuko/.../bold" failed, and cd to bold didn't work either (error message pasted below). Then, Mark suggested me to replace /fsfast/bin/getrunlist with the one from v4.5.0., which solved the problem. Thank you Doug & Mark! Yuko Yotsumoto %--- getrunlist /Users/yuko/

Re: [Freesurfer] preproc-sess error in version 5.0

Hi Yuko, can you try running: getrunlist /Users/yuko/Documents/FreeSurfer/sessions/VM/VM20/bold If that fails, try this: cd /Users/yuko/Documents/FreeSurfer/sessions/VM/VM20/bold doug yuko YY wrote: > Hello, > > I recently switch to version 5, and am having a problem with > preproc-sess in v

Re: [Freesurfer] preproc-sess failing

Hi Doug, That did the trick! Thanks so much! -Adam > Hi Adam, the problem is that the original fmc.nii was generated with an > error because of the lack of disc space. But the file itself exists and > has a creation date after f.nii, so preproc-sess did not know that there > was anything wrong w

Re: [Freesurfer] preproc-sess failing

Hi Adam, the problem is that the original fmc.nii was generated with an error because of the lack of disc space. But the file itself exists and has a creation date after f.nii, so preproc-sess did not know that there was anything wrong with it and did not try to regenerate it. Try deleting fmc.

Re: [Freesurfer] preproc-sess in v5

You're right that, at least in one situation, theory says it should make little effect. That situation is when you go to do a simple random effects group analysis. It will have an effect if you use the first level estimates of the variance for anything. This includes looking at individual subje

Re: [Freesurfer] preproc-sess failing

Hi Doug, My original email was sent to the freesurfer list. Here is the more detailed terminal info: FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4_x86_64-stable-v4.5.0-20100311 RedHat release: CentOS release 5.5 (Final) Kernel info: Linux 2.6.18-194.8.1.

Re: [Freesurfer] preproc-sess error

If you're going to continue to use stable3 then you will need to have an old version of FSL (the ip program is an FSL program from several versions ago). Can you start using the new version of FSFAST? doug swood...@nmr.mgh.harvard.edu wrote: > Additional info: > > FREESURFER_HOME: /usr/local/fr

Re: [Freesurfer] preproc-sess error

Additional info: FREESURFER_HOME: /usr/local/freesurfer/stable3 Build stamp: freesurfer-Linux-centos4_x86_64-stable-v3.0.5-20070714 RedHat release: CentOS release 5.5 (Final) Kernel info: Linux 2.6.18-194.8.1.el5 x86_64 NMR Center info (/space/freesurfer exists): Does this give you the info y

Re: [Freesurfer] preproc-sess error

which version are you using? swood...@nmr.mgh.harvard.edu wrote: > Hello everyone, > > I keep encountering the same error when running some preprocessing steps > (spatial smooting part). > > I run the command line: > > preproc-sess -s CD_DMRFASL_pat4 -df sessdirfile -mcout fmc5 -fwhm 5 -smin > fmc

Re: [Freesurfer] "preproc-sess" failing at 3dvolreg

does that file exist? Did that disk run out of space? Krishna Srihasam wrote: Hi, I am trying to analyze my fMRI data ( collected at MGH) using FSFAST and I was following the tutrial (http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastWorkFlows). I was able to unpack the data. But when I run "pre

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