[Freesurfer] blend own template into FS pipeline
Hi FreeSurfer experts, We are dealing with a sample of children MRI and we want to introduce our own templates into the pipeline instead of the MNI/tailarach. Any advice or guidance you can provide on how to go about doing this would be much appreciate it. Thanks, Kev ___ 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 whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] blend own template into FS pipeline
I would like to play with both normalization and registration steps, and contrast results. Thanks, Kev On Mon, Feb 25, 2013 at 6:03 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Kev for what purpose? If it's just for talairaching, Avi (ccd) is the person to ask cheers Bruce On Mon, 25 Feb 2013, Schumman Resonance wrote: Hi FreeSurfer experts, We are dealing with a sample of children MRI and we want to introduce our own templates into the pipeline instead of the MNI/tailarach. Any advice or guidance you can provide on how to go about doing this would be much appreciate it. Thanks, Kev The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ 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 whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Estimate of number of manual edits and time to complete in 100subject sample
This is a question for the FS community in general, I gather there is variability around this, but rather than an exact number and time, I was hoping for an estimate on how many scans would I expect to require manual edits(any of the check points recommended in the tutorials) as well as an estimate of the time it takes to go through them. For the sake of the argument, take a sample of 100 subjects. Thanks, Kev ___ 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 whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] mri_convert mnc to nii
Hi freesurfers, I want to convert minc files to nii to work with them in ITK-SNAP segmentation software. I have used mri_convert binary, but the orientation on the nii images is completely wonky. Any advice in terms of how to use the --in_orientation argument --out_orientation argument flags? Reading the documentation on the FS wiki emphasizes how important is to get this right. Any pointers will be much appreciate it. Thanks, Fidel ___ 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 whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] TAR fs files
Thanks for the quick responses; I appreciate it. I gather that is exactly what the message is telling, but It is very odd as I'm positive I was not doing anything with the files and it showed the same message for each of the subjects and for each of the tailrace files on X,Y,Z. In any case, it is reassuring to know those files have no use once everything has been run. Cheers On Wed, Jul 12, 2017 at 4:20 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > hmmm, that doesn't sound like it has anything to do with us unless you > were running a recon when you were tarring. That file is mostly irrelevant > in any case > > cheers > Bruce > > > On Wed, 12 Jul 2017, Schumman > Resonance wrote: > > > Hi freesurfers, > > I'm compressing FS files for storage, and while runnig TAR I got this > > message for all the files in the directory I'm compressing: > > > > "tar: data/sbj001_post_anat.nii.gz/mri/transforms/talairach.m3z. > inv.y.mgz: > > file changed as we read it" > > > > Any thoughts on whether this message is making any changes on those > tailrace > > files so that when I decompress the file I do not get the original > > information in those files. > > > > Thanks for your help/advice, > > > > Kev > > > > > > > > > > > > > ___ > 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 whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ 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 whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] TAR fs files
Hi freesurfers, I'm compressing FS files for storage, and while runnig TAR I got this message for all the files in the directory I'm compressing: "tar: data/sbj001_post_anat.nii.gz/mri/transforms/talairach.m3z.inv.y.mgz: file changed as we read it" Any thoughts on whether this message is making any changes on those tailrace files so that when I decompress the file I do not get the original information in those files. Thanks for your help/advice, Kev ___ 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 whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] content of "subjects_dir"
Dear free surfer community, Silly question here. I note the default "subjects_dir" in freesurfer contains a bunch of directories and files. If I set the environment so that my "subjects_dir" is not the default location, do I need to move any of the files in the original location to the new one? I hope this makes sense. Thanks, Kev ___ 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 whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Freeview error
Hi, Newbie question. When I try to upload a surface to Freview I get the following error: [0]PETSC ERROR: [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file [unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 Thanks, Kev ___ 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 whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Freeview error
Attached is the full command line; as per a screen output Freeview quits. I have not tested all surface files, but Freeview uploads fine pial, white, inflated, orig, and sphere. Thanks! On Sat, May 27, 2017 at 8:46 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > Can you send us the full command line and screen output? > Cheers > Bruce > > On May 27, 2017, at 11:45 PM, Schumman Resonance <schumm...@gmail.com> > wrote: > > Hi, > > Newbie question. > > When I try to upload a surface to Freview I get the following error: > > > [0]PETSC ERROR: -- > -- > > [0]PETSC ERROR: User provided function() line 0 in unknown directory > unknown file > > [unset]: aborting job: > > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 > > > Thanks, > Kev > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ > 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 whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > Freeview_error_May2017 Description: Binary data ___ 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 whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Untar and sh files in dev version
External Email - Use Caution Hi, Couple of newbie questions. I downloaded the dev version of freesurfer and did: tar xvzf freesurfer-linux-centos6_x86_64-dev.tar.gz to get gzip: stdin: unexpected end of file tar: Unexpected EOF in archive tar: Unexpected EOF in archive tar: Error is not recoverable: exiting now Also, when I ls the folder I couldn't see the SetUpFreesurfer.sh and SurferEnv.sh only the csh files. Any pointers how to solve these would be appreciated. Thanks, S ___ 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 whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Untar and sh files in dev version
External Email - Use Caution Thanks for your response. I run the command you suggested and this is what I got: freesurfer/average/mult-comp-cor/fsaverage_sym/rh/cortex/fwhm04/pos/th33/mc-z.csd: (Empty error message) tar: Error exit delayed from previous errors. Also, still no .sh files... Best, K On Fri, Aug 10, 2018 at 7:52 PM, Dicamillo, Robert < rdicami...@mgh.harvard.edu> wrote: > Hello Schumman, > > Try the following command on the tar archive (cut and paste it if you like) > > $ tar zxpf freesurfer-linux-centos6_x86_64-dev.tar.gz > > and then take a look at the files. > > - Rob > > On Aug 10, 2018, at 10:25 PM, Schumman Resonance > wrote: > > External Email - Use Caution > > Hi, > > Couple of newbie questions. I downloaded the dev version of freesurfer > and did: > tar xvzf > freesurfer-linux-centos6_x86_64-dev.tar.gz > > to get > > > gzip: stdin: unexpected end of file > tar: Unexpected EOF in archive > tar: Unexpected EOF in archive > tar: Error is not recoverable: exiting now > > > > Also, when I ls the folder I couldn't see the SetUpFreesurfer.sh and > SurferEnv.sh only the csh files. > > Any pointers how to solve these would be appreciated. > > Thanks, > S > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > ___ > 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 whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ 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 whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Untar and sh files in dev version
External Email - Use Caution Thanks for your response, but I already have the stable release version in another system. What I'd like to do now is to run the development version. Thanks, K On Sat, Aug 11, 2018 at 1:22 AM, Dicamillo, Robert < rdicami...@mgh.harvard.edu> wrote: > Hello K, > > Can you try downloading the 6.0.0 release archive from the web site > (please note it is 4.8G), > > freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz > <ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz> > > Then you will need 5 GB of space to uncompress it. I would add the v > option so you can see the expansion in progress, > > $ tar zxvpf freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz > > - Rob > > > On Aug 11, 2018, at 2:55 AM, Schumman Resonance > wrote: > > External Email - Use Caution > > Thanks for your response. > I run the command you suggested and this is what I got: > freesurfer/average/mult-comp-cor/fsaverage_sym/rh/cortex/fwhm04/pos/th33/mc-z.csd: > (Empty error message) > tar: Error exit delayed from previous errors. > > Also, still no .sh files... > > Best, > K > > On Fri, Aug 10, 2018 at 7:52 PM, Dicamillo, Robert < > rdicami...@mgh.harvard.edu> wrote: > >> Hello Schumman, >> >> Try the following command on the tar archive (cut and paste it if you >> like) >> >> $ tar zxpf freesurfer-linux-centos6_x86_64-dev.tar.gz >> >> and then take a look at the files. >> >> - Rob >> >> On Aug 10, 2018, at 10:25 PM, Schumman Resonance >> wrote: >> >> External Email - Use Caution >> >> Hi, >> >> Couple of newbie questions. I downloaded the dev version of freesurfer >> and did: >> tar xvzf >> freesurfer-linux-centos6_x86_64-dev.tar.gz >> >> to get >> >> >> gzip: stdin: unexpected end of file >> tar: Unexpected EOF in archive >> tar: Unexpected EOF in archive >> tar: Error is not recoverable: exiting now >> >> >> >> Also, when I ls the folder I couldn't see the SetUpFreesurfer.sh and >> SurferEnv.sh only the csh files. >> >> Any pointers how to solve these would be appreciated. >> >> Thanks, >> S >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> ___ >> 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 whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you >> in error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > ___ > 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 whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ 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 whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Stats2table_bash.sh script
External Email - Use Caution Hi, I'm trying to run the Stats2table_bash.sh script from Jamaan Alghamdi & Dr. Vanessa Sluming. And I get This error: File "/Applications/freesurfer/bin/asegstats2table", line 195 print 'ERROR: subjects are not specified (use --subjects SUBJECTS)' ^ SyntaxError: invalid syntax File "/Applications/freesurfer/bin/asegstats2table", line 195 print 'ERROR: subjects are not specified (use --subjects SUBJECTS)' ^ SyntaxError: invalid syntax File "/Applications/freesurfer/bin/aparcstats2table", line 156 print 'ERROR: atleast 1 subject must be provided' . . . This is my set up: _ freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Users/schumman/data MNI_DIR /Applications/freesurfer/mni FSL_DIR /usr/local/fsl _ This is the line from SetUpFreeSurfer.sh for my subjects directory # Set this to your subjects/ dir, usually freesurfer/subjects/ if [ -z $SUBJECTS_DIR ]; then export SUBJECTS_DIR=/Users/schumman/data __ And I modified in their script to my FREESURFER_HOME as below #!/bin/bash path=`dirname $0` sleep 1 cd $path echo "This bash script will create table from ?.stats files" echo "Written by Jamaan Alghamdi & Dr. Vanessa Sluming" echo "University of Liverpool" echo "jamaan.algha...@gmail.com" echo "http://www.easyneuroimaging.com; echo "20/12/2010 " export FREESURFER_HOME=/Applications/freesurfer sleep 1 source $FREESURFER_HOME/SetUpFreeSurfer.sh sleep 1 export SUBJECTS_DIR=$PWD list="`ls -d */`" asegstats2table --subjects $list --meas volume --skip --statsfile wmparc.stats --all-segs --tablefile wmparc_stats.txt . . . I run the script from my_subject_directory. I suspect this is something very obvious I'm not able to see and I apologize for such a basic question, any help would be much appreciated. Thanks, K ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Stats2table_bash.sh script
External Email - Use Caution Thanks Robert, I guess my main issue is that I don't fully understand how the script works: [1] export SUBJECTS_DIR=*$PWD* *[2] list="`ls -d */`"* [3] asegstats2table --subjects *$list *--meas volume --skip --statsfile wmparc.stats --all-segs --tablefile wmparc_stats.txt I was assuming the variable $list would give SUBJECTS to --subjects based on each directory where .stats files are. I don't fully understand how lines [1] and [2] work. Apologies if I'm not conveying my struggle with proper coding language :) On Sun, Aug 12, 2018 at 2:03 PM, Dicamillo, Robert < rdicami...@mgh.harvard.edu> wrote: > Hello K, > > If you type > > $ asegstats2table --help > > you will see that you can specify subjects on the command line as, e.g., > for bert as > > —subjects bert > or apparently > -s bert > > It looks like the subjects option expects the name for at least one > subjects (data), > but the help output says you can list more than one subjects name as the > argument to > —subjects > > On Aug 12, 2018, at 12:31 PM, Schumman Resonance > wrote: > > External Email - Use Caution > > > Hi, > > I'm trying to run the Stats2table_bash.sh script from Jamaan Alghamdi & > Dr. Vanessa Sluming. > > And I get This error: > > File "/Applications/freesurfer/bin/asegstats2table", line 195 > print 'ERROR: subjects are not specified (use --subjects SUBJECTS)' > ^ > SyntaxError: invalid syntax > File "/Applications/freesurfer/bin/asegstats2table", line 195 > print 'ERROR: subjects are not specified (use --subjects SUBJECTS)' > ^ > SyntaxError: invalid syntax > File "/Applications/freesurfer/bin/aparcstats2table", line 156 > print 'ERROR: atleast 1 subject must be provided' > . > . > . > > > > This is my set up: > > > _ > > > freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c > Setting up environment for FreeSurfer/FS-FAST (and FSL) > FREESURFER_HOME /Applications/freesurfer > FSFAST_HOME /Applications/freesurfer/fsfast > FSF_OUTPUT_FORMAT nii.gz > SUBJECTS_DIR /Users/schumman/data > MNI_DIR /Applications/freesurfer/mni > FSL_DIR /usr/local/fsl > > _ > > > This is the line from SetUpFreeSurfer.sh for my subjects directory > > > # Set this to your subjects/ dir, usually freesurfer/subjects/ > if [ -z $SUBJECTS_DIR ]; then > export SUBJECTS_DIR=/Users/schumman/data > > > __ > > And I modified in their script to my FREESURFER_HOME as below > > > #!/bin/bash > path=`dirname $0` > sleep 1 > cd $path > echo "This bash script will create table from ?.stats files" > echo "Written by Jamaan Alghamdi & Dr. Vanessa Sluming" > echo "University of Liverpool" > echo "jamaan.algha...@gmail.com" > echo "http://www.easyneuroimaging.com; > echo "20/12/2010 > > " > > > export FREESURFER_HOME=/Applications/freesurfer > sleep 1 > source $FREESURFER_HOME/SetUpFreeSurfer.sh > sleep 1 > > export SUBJECTS_DIR=$PWD > list="`ls -d */`" > asegstats2table --subjects $list --meas volume --skip --statsfile > wmparc.stats --all-segs --tablefile wmparc_stats.txt > . > . > . > > > I run the script from my_subject_directory. > > I suspect this is something very obvious I'm not able to see and I > apologize for such a basic question, any help would be much appreciated. > > Thanks, > K > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > ___ > 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 whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > p
Re: [Freesurfer] Untar and sh files in dev version
External Email - Use Caution Thanks Andrew. I have done that twice now... On Sat, Aug 11, 2018 at 10:21 AM, Hoopes, Andrew wrote: > Hi K, your original error is usually due to an incomplete download. You > might want to try redownloading and untaring again > > Best, > > Andrew > > > > *From: * on behalf of Schumman > Resonance > *Reply-To: *FS Help > *Date: *Saturday, August 11, 2018 at 9:24 AM > *To: *FS Help > *Subject: *Re: [Freesurfer] Untar and sh files in dev version > > > > *External Email - Use Caution* > > Thanks for your response, but I already have the stable release version in > another system. > > What I'd like to do now is to run the development version. > > Thanks, > > K > > > > > > On Sat, Aug 11, 2018 at 1:22 AM, Dicamillo, Robert < > rdicami...@mgh.harvard.edu> wrote: > > Hello K, > > > > Can you try downloading the 6.0.0 release archive from the web site > (please note it is 4.8G), > > > > freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz > <ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz> > > > > Then you will need 5 GB of space to uncompress it. I would add the v > option so you can see the expansion in progress, > > > > $ tar zxvpf freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz > > > > - Rob > > > > > > On Aug 11, 2018, at 2:55 AM, Schumman Resonance > wrote: > > > > *External Email - Use Caution* > > > > Thanks for your response. > > I run the command you suggested and this is what I got: > > freesurfer/average/mult-comp-cor/fsaverage_sym/rh/cortex/fwhm04/pos/th33/mc-z.csd: > (Empty error message) > > tar: Error exit delayed from previous errors. > > > > Also, still no .sh files... > > > > Best, > > K > > > > On Fri, Aug 10, 2018 at 7:52 PM, Dicamillo, Robert < > rdicami...@mgh.harvard.edu> wrote: > > Hello Schumman, > > > > Try the following command on the tar archive (cut and paste it if you like) > > > > $ tar zxpf freesurfer-linux-centos6_x86_64-dev.tar.gz > > > > and then take a look at the files. > > > > - Rob > > > > On Aug 10, 2018, at 10:25 PM, Schumman Resonance > wrote: > > > > *External Email - Use Caution* > > > > Hi, > > > > Couple of newbie questions. I downloaded the dev version of freesurfer > and did: > > tar xvzf > > freesurfer-linux-centos6_x86_64-dev.tar.gz > > > > to get > > > > > > gzip: stdin: unexpected end of file > > tar: Unexpected EOF in archive > > tar: Unexpected EOF in archive > > tar: Error is not recoverable: exiting now > > > > > > > > Also, when I ls the folder I couldn't see the SetUpFreesurfer.sh and > SurferEnv.sh only the csh files. > > > > Any pointers how to solve these would be appreciated. > > > > Thanks, > > S > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > ___ > 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 whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > ___ > 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 whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patie
[Freesurfer] is untar existing runtime2012b.tar.gz sufficient?
Hi, I was following the steps on the wiki to run the hipposubfields stream and it mentioned runtime needs to be downloaded. However, I noticed in my free surfer home the tar file runtime2012b.tar.gz. Would untaring this existing file in fresurfer homer put the libraries required in the MCR folder, I do I still need to download runtime? Thanks and best regards, Kev ___ 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 whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
