Re: [Freesurfer] iPhone and IPad FreeSurfer based atlas
http://itunes.apple.com/us/app/isurf-brainview/id381072423?mt=8 The download link for United States -- via iPhone iOS4 Em 22/09/2010, às 20:50, Nick Schmansky escreveu: > > On Wed, 2010-09-22 at 19:17 -0300, Pedro Paulo de Magalhães Oliveira > Junior wrote: >> More news on the free brain atlas app for IPhone using FreeSurfer >> aseg. >> >> Today we have another major upgrade: >> >> >> - Pinch and Zoom >> - Many papers for Reading >> - Improved documentation of FreeSurfer >> >> http://itunes.apple.com/br/app/isurf-brainview/id381072423?mt=8 >> >> Suggestions for the upcoming version are welcome. >> >> Cheers >> >> Pedro Paulo Jr. >> >> -- via iPhone iOS4 >> - >> Pedro Paulo de Magalhães Oliveira Junior >> Diretor de Operações >> Netfilter & SpeedComm Telecom >> -- www.netfilter.com.br >> -- For mobile: http://www.netfilter.com.br/mobile >> >> >> >> >> ___ >> 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
Re: [Freesurfer] -legacy
yes, the -legacy flag was only necessary for the v3.0 to v4.0 transition. v4.0 data should be fully compatible with reprocessing in v5. n. On Wed, 2010-09-22 at 17:31 -0500, Juranek, Jenifer wrote: > I'm hoping to push my legacy datasets (processed and edited in FSv4.0.5) > through FSv5.0.0. After installing FSv5.0.0, I received an error that it > didn't look like a legacy analysis (see below). > [jjura...@localhost subjects]$ recon-all -legacy -s SB_057_H21001 > ERROR: you have specified -legacy, but this does not look like >a legacy analysis. > > My recon-all.log file for this subjid reports the following build-stamp.txt: > freesurfer-Linux-centos4_x86_64-stable-pub-v4.0.5 > > How do I convince FSv5.0.0 that I am feeding it legacy data from FSv4.0.5? > Have I skipped too many versions to use this -legacy flag? > > Many thanks, > Jenifer > > > ___ > 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] -legacy
I'm hoping to push my legacy datasets (processed and edited in FSv4.0.5) through FSv5.0.0. After installing FSv5.0.0, I received an error that it didn't look like a legacy analysis (see below). [jjura...@localhost subjects]$ recon-all -legacy -s SB_057_H21001 ERROR: you have specified -legacy, but this does not look like a legacy analysis. My recon-all.log file for this subjid reports the following build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v4.0.5 How do I convince FSv5.0.0 that I am feeding it legacy data from FSv4.0.5? Have I skipped too many versions to use this -legacy flag? Many thanks, Jenifer ___ 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] iPhone and IPad FreeSurfer based atlas
More news on the free brain atlas app for IPhone using FreeSurfer aseg. Today we have another major upgrade: - Pinch and Zoom - Many papers for Reading - Improved documentation of FreeSurfer http://itunes.apple.com/br/app/isurf-brainview/id381072423?mt=8 Suggestions for the upcoming version are welcome. Cheers Pedro Paulo Jr. -- via iPhone iOS4 - Pedro Paulo de Magalhães Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://www.netfilter.com.br/mobile ___ 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] System requirements
the second option is best because it uses the x86 processor (amd opteron), which is our common distribution. the first option uses the Itanium processor which we dont actively support because we no longer have access to a build machine. the recon-all stream is not parallelized so you wouldnt benefit from multi-cores or any special parallelization hardware. runtime on the amd cluster would be about 25 hours per subject, and consume a peak of about 2.7GB of ram. each subject consumes around 400MB of hard disk space (budget 500MB per subject). negligible temporary hard disk space is used. n. On Wed, 2010-09-22 at 19:17 +0200, daniel geisler wrote: > Dear Freesurfers! > > I am a new user of freesurfer and I intend to install it on a HPC > system. There are two different systems available (see end of > message). Could you please give me a hint which one is best suited wrt > hardware and software. > > In order to use these systems one also has to state some estimations > of the needed resources. In detail, I have to estimate: > > * CPU time > * maximal number of parallel used CPUs > * size of used RAM > * size of permanent HDD usage > * size of temporary HDD usage > > Could you share some experience how many resources are usually used > for the segmentation (recon-all) of a single subject? > > Thank you & best wishes from Dresden, > Daniel > > --- > 1.SGI Altix 4700 (Mars) > > * For highly parallel and memory-intensive applications > * 2048 cores Intel Itanium II Montecito 1.6 GHz > * 6,5 TB memory > * One partition for interactive operation with 128 cores > * 68 TB SAN disk storage > * 1 PB SAN tape archive > * SuSE Linux Enterprise Server 10, SGI ProPack 5, batch system LSF > * 13,1 TFlop/s peak performance > > 2. Linux Networx Evolocity II PC-Farm (Deimos) > > * For capacity computing > * 2576 cores AMD Opteron 2,6 GHz > * 5,4 TB memory > * 724 nodes with 1, 2, or 4 dual-core CPUs each > * 68 TB SAN disk storage > * SuSE Linux Enterprise Server 10, batch system LSF > * 13,9 TFlop/s peak performance > > For software specification please refer to: > http://tu-dresden.de/die_tu_dresden/zentrale_einrichtungen/zih/hpc/hochleistungsrechner/hpc_software?set_language=en&cl=en > ___ > 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.
Re: [Freesurfer] isxconcat question
Hi Mo, It means that you have an old version of fsaverage in your SUBJECTS_DIR or linked to your SUBJECTS_DIR. Try using the one in $FREESURFER_HOME/subjects/fsaverage doug Zeidan, Mohamed A. wrote: > I got the following error when running isxconcat-sess: > > ERROR: cannot find > /space/grouch/3/users/ext/fsaverage/mri.2mm/subcort.mask.mgz > > I've never seen this before, but this is my first time using isxconcat in > fsfast > v. 5. > > Anyone know how to fix it? > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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] System requirements
Dear Freesurfers! I am a new user of freesurfer and I intend to install it on a HPC system. There are two different systems available (see end of message). Could you please give me a hint which one is best suited wrt hardware and software. In order to use these systems one also has to state some estimations of the needed resources. In detail, I have to estimate: * CPU time * maximal number of parallel used CPUs * size of used RAM * size of permanent HDD usage * size of temporary HDD usage Could you share some experience how many resources are usually used for the segmentation (recon-all) of a single subject? Thank you & best wishes from Dresden, Daniel --- 1.SGI Altix 4700 (Mars) * For highly parallel and memory-intensive applications * 2048 cores Intel Itanium II Montecito 1.6 GHz * 6,5 TB memory * One partition for interactive operation with 128 cores * 68 TB SAN disk storage * 1 PB SAN tape archive * SuSE Linux Enterprise Server 10, SGI ProPack 5, batch system LSF * 13,1 TFlop/s peak performance 2. Linux Networx Evolocity II PC-Farm (Deimos) * For capacity computing * 2576 cores AMD Opteron 2,6 GHz * 5,4 TB memory * 724 nodes with 1, 2, or 4 dual-core CPUs each * 68 TB SAN disk storage * SuSE Linux Enterprise Server 10, batch system LSF * 13,9 TFlop/s peak performance For software specification please refer to: http://tu-dresden.de/die_tu_dresden/zentrale_einrichtungen/zih/hpc/hochleistungsrechner/hpc_software?set_language=en&cl=en ___ 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] GLM question
There is not a command-line program to do this. You can do it inside of tksurfer. You can also load your significance maps into matlab, convert to p-value, then use fast_fdrthresh.m doug Gabriel Go.Es. wrote: > > Hello everybody > I'm wondering about how to perform an FDR correction using the glmfit > on FS?, I mean using command line if there is one; > And Could it be applied the same sentence to correct at cortex level > and clusters label, or need some special arguments on the command line > for any of them? > > Thanks in advance > Gabriel > > > > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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] nframes file parameter...
you can use mri_convert --frame 0 to get the 1st frame. doug Gonzalo Rojas Costa wrote: > Hi Bruce: > > And how can I get only one frame ?... I don't know why the medical > technologist got the two frames... > > Sincerely, > > > Gonzalo Rojas Costa > > > Bruce Fischl escribió: > >> the 2nd one is a 4D volume with 2 frames (each of which is 256x256x176) >> >> cheers >> Bruce >> On >> Wed, 22 Sep 2010, Gonzalo Rojas Costa wrote: >> >> >>> Hi: >>> >>> What it means the "nframes" parameter ?... Which is the difference between >>> a >>> 001 mgz file that has "dimensions: 256 x 256 x 176" and another that has >>> "dimensions: 256 x 256 x 176 x 2" ?... >>> >>> Sincerely, >>> >>> >>> Gonzalo Rojas Costa >>> >>> ___ >>> 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. >> >> >> > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] QDEC table loading errors
there shouldn't be a limit on the number of columns it will read. the
thing to be careful about is the name of a column. sometimes when
importing a spreadsheet, a column name will consist of two words (thus
messing-up the detected number of columns), or it will have a minus "-"
char in the name, which doesnt get interpreted properly. probably there
is a column name which is not a single word.
n.
On Wed, 2010-09-22 at 10:45 -0500, James Porter wrote:
> Of course, once I ask for help I stumble immediately upon the
> solution. There appears to be a limit to the number of columns that
> QDEC is willing to put up with when reading in tables. If I create a
> table that only has the few columns that I'm interested in (as opposed
> to the kitchen sink spreadsheet I was working with), then it reads in
> without error.
>
> Thanks for the help by proxy!
> Jim
>
>
> On 9/22/10 10:38 AM, Nick Schmansky wrote:
> > can you send me the file?
> >
> > n.
> >
> > On Wed, 2010-09-22 at 10:28 -0500, James Porter wrote:
> > > Hello-
> > >
> > > I'm having a resurgence of an old problem
> > > (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg12152.html)
> > > but the old solution is not cutting it. When I try to load a table in
> > > QDEC 1.4, I get the following error:
> > >
> > > Loading data table qdec.table.dat...
> > > ERROR: QdecDataTable::Load did not find a column named 'fsid',
> > > 'ID', or 'Subject' in the first column of qdec.table.dat!
> > > Error loading the data table.
> > >
> > > However, the file definitely does have 'fsid' as the first column.
> > >
> > > > head qdec.table.dat | awk '{print $1, $2, $3}'
> > > fsid Sex AgeGrp
> > > 14080 Female Oldr
> > > 14081 Female Oldr
> > > 14286 Female Oldr
> > > 14287 Female Oldr
> > > 14390 Female Oldr
> > > 14391 Male Oldr
> > > 14392 Male Oldr
> > > 14428 Female Oldr
> > > 14430 Male Oldr
> > >
> > > Creating the file on Windows, Mac, and Unix platforms using a variety
> > > of programs (kate, oocalc, text wrangler, excel, word, notepad, etc)
> > > with 'fsid', 'ID', or 'Subject' as the column title doesn't help, nor
> > > does running dos2unix on the file(s). Having tab delimited or space
> > > delimited files doesn't make any difference, either. Trying to open
> > > the tables with QDEC in Unix (RedHat) or Mac (10.6.4) doesn't change
> > > the outcome.
> > >
> > > Any ideas on how to solve this riddle?
> > >
> > > Thanks,
> > > Jim
> > > --
> > > Jim Porter, M.A.
> > > Graduate Student
> > > Clinical Science and Psychopathology Research
> > > University of Minnesota
> > >
> > > ___
> > > 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.
> >
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Re: [Freesurfer] nframes file parameter...
Hi Bruce: And how can I get only one frame ?... I don't know why the medical technologist got the two frames... Sincerely, Gonzalo Rojas Costa Bruce Fischl escribió: > the 2nd one is a 4D volume with 2 frames (each of which is 256x256x176) > > cheers > Bruce > On > Wed, 22 Sep 2010, Gonzalo Rojas Costa wrote: > >> Hi: >> >> What it means the "nframes" parameter ?... Which is the difference between >> a >> 001 mgz file that has "dimensions: 256 x 256 x 176" and another that has >> "dimensions: 256 x 256 x 176 x 2" ?... >> >> Sincerely, >> >> >> Gonzalo Rojas Costa >> >> ___ >> 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
Re: [Freesurfer] nframes file parameter...
the 2nd one is a 4D volume with 2 frames (each of which is 256x256x176) cheers Bruce On Wed, 22 Sep 2010, Gonzalo Rojas Costa wrote: > Hi: > > What it means the "nframes" parameter ?... Which is the difference between a > 001 mgz file that has "dimensions: 256 x 256 x 176" and another that has > "dimensions: 256 x 256 x 176 x 2" ?... > > Sincerely, > > > Gonzalo Rojas Costa > > ___ > 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.
Re: [Freesurfer] QDEC table loading errors
Of course, once I ask
for help I stumble immediately upon the solution. There appears to
be a limit to the number of columns that QDEC is willing to put up
with when reading in tables. If I create a table that only has the
few columns that I'm interested in (as opposed to the kitchen sink
spreadsheet I was working with), then it reads in without
error.
Thanks for the help by proxy!
Jim
On 9/22/10 10:38 AM, Nick Schmansky wrote:
can you send me the file?
n.
On Wed, 2010-09-22 at 10:28 -0500, James Porter wrote:
Hello-
I'm having a resurgence of an old problem
(http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg12152.html) but the old solution is not cutting it. When I try to load a table in QDEC 1.4, I get the following error:
Loading data table qdec.table.dat...
ERROR: QdecDataTable::Load did not find a column named 'fsid',
'ID', or 'Subject' in the first column of qdec.table.dat!
Error loading the data table.
However, the file definitely does have 'fsid' as the first column.
> head qdec.table.dat | awk '{print $1, $2, $3}'
fsid Sex AgeGrp
14080 Female Oldr
14081 Female Oldr
14286 Female Oldr
14287 Female Oldr
14390 Female Oldr
14391 Male Oldr
14392 Male Oldr
14428 Female Oldr
14430 Male Oldr
Creating the file on Windows, Mac, and Unix platforms using a variety
of programs (kate, oocalc, text wrangler, excel, word, notepad, etc)
with 'fsid', 'ID', or 'Subject' as the column title doesn't help, nor
does running dos2unix on the file(s). Having tab delimited or space
delimited files doesn't make any difference, either. Trying to open
the tables with QDEC in Unix (RedHat) or Mac (10.6.4) doesn't change
the outcome.
Any ideas on how to solve this riddle?
Thanks,
Jim
--
Jim Porter, M.A.
Graduate Student
Clinical Science and Psychopathology Research
University of Minnesota
___
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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.
___
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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] nframes file parameter...
Hi: What it means the "nframes" parameter ?... Which is the difference between a 001 mgz file that has "dimensions: 256 x 256 x 176" and another that has "dimensions: 256 x 256 x 176 x 2" ?... Sincerely, Gonzalo Rojas Costa ___ 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] QDEC table loading errors
can you send me the file?
n.
On Wed, 2010-09-22 at 10:28 -0500, James Porter wrote:
> Hello-
>
> I'm having a resurgence of an old problem
> (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg12152.html)
> but the old solution is not cutting it. When I try to load a table in QDEC
> 1.4, I get the following error:
>
> Loading data table qdec.table.dat...
> ERROR: QdecDataTable::Load did not find a column named 'fsid',
> 'ID', or 'Subject' in the first column of qdec.table.dat!
> Error loading the data table.
>
> However, the file definitely does have 'fsid' as the first column.
>
> > head qdec.table.dat | awk '{print $1, $2, $3}'
> fsid Sex AgeGrp
> 14080 Female Oldr
> 14081 Female Oldr
> 14286 Female Oldr
> 14287 Female Oldr
> 14390 Female Oldr
> 14391 Male Oldr
> 14392 Male Oldr
> 14428 Female Oldr
> 14430 Male Oldr
>
> Creating the file on Windows, Mac, and Unix platforms using a variety
> of programs (kate, oocalc, text wrangler, excel, word, notepad, etc)
> with 'fsid', 'ID', or 'Subject' as the column title doesn't help, nor
> does running dos2unix on the file(s). Having tab delimited or space
> delimited files doesn't make any difference, either. Trying to open
> the tables with QDEC in Unix (RedHat) or Mac (10.6.4) doesn't change
> the outcome.
>
> Any ideas on how to solve this riddle?
>
> Thanks,
> Jim
> --
> Jim Porter, M.A.
> Graduate Student
> Clinical Science and Psychopathology Research
> University of Minnesota
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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
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[Freesurfer] QDEC table loading errors
Hello-
I'm having a resurgence of an old problem
(http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg12152.html)
but the old solution is not cutting it. When I try to load a table
in QDEC 1.4, I get the following error:
Loading data table qdec.table.dat...
ERROR: QdecDataTable::Load did not find a column named 'fsid',
'ID', or 'Subject' in the first column of qdec.table.dat!
Error loading the data table.
However, the file definitely does have 'fsid' as the first column.
> head qdec.table.dat | awk '{print $1, $2, $3}'
fsid Sex AgeGrp
14080 Female Oldr
14081 Female Oldr
14286 Female Oldr
14287 Female Oldr
14390 Female Oldr
14391 Male Oldr
14392 Male Oldr
14428 Female Oldr
14430 Male Oldr
Creating the file on Windows, Mac, and Unix platforms using a
variety of programs (kate, oocalc, text wrangler, excel, word,
notepad, etc) with 'fsid', 'ID', or 'Subject' as the column title
doesn't help, nor does running dos2unix on the file(s). Having tab
delimited or space delimited files doesn't make any difference,
either. Trying to open the tables with QDEC in Unix (RedHat) or
Mac (10.6.4) doesn't change the outcome.
Any ideas on how to solve this riddle?
Thanks,
Jim
--
Jim Porter, M.A.
Graduate Student
Clinical Science and Psychopathology Research
University of Minnesota
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[Freesurfer] GLM question
Hello everybody I'm wondering about how to perform an FDR correction using the glmfit on FS?, I mean using command line if there is one; And Could it be applied the same sentence to correct at cortex level and clusters label, or need some special arguments on the command line for any of them? Thanks in advance Gabriel ___ 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] changing f.nii nframes
The 'fsledithd' utility (of FSL) can be used to edit the number of frames (as well as a host of other fields) in a Nifti file. cheers, -MH On Wed, 2010-09-22 at 09:02 -0400, Douglas Greve wrote: > Hi Tommi, that's going to be a problem because all the tools look at > the number of frames to determine how much data to read in (unlike voxel > size or direction cosines). I don't know of an easy way around it, > though I can think of some hard ones. How hard is it to fix the grappa > recon to write out the right number of frames? > > doug > > On 9/22/10 1:35 AM, r...@nmr.mgh.harvard.edu wrote: > > Dear Free Surfers, > > > > I am analyzing fMRI time series that were reconstructed offline (GRAPPA > > data that needed some artifact corrections, long story). Unfortunately, > > the offline reconstructed f.nii do not include proper header info. I think > > I was able to set the orientations correctly using mri_convert, but now > > FSFAST preprocessing (specifically, mc-sess) fails because the headers say > > that the number of TRs (number of full volume acquisitions) in the > > measurement is 1, whereas in fact the correct value is 316. > > > > I could not find a tool that could change the "nframes" value (mri_convert > > can adjust many other things but not this one it seems). Any suggestions? > > > > > > Bests, > > > > Tommi > > > > > > --- > > Tommi Raij, M.D., Ph.D. > > MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging > > Bldg 149, 13th St > > Charlestown, MA 02129 > > U.S.A. > > > > ___ > > 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
Re: [Freesurfer] changing f.nii nframes
Hi Tommi, that's going to be a problem because all the tools look at the number of frames to determine how much data to read in (unlike voxel size or direction cosines). I don't know of an easy way around it, though I can think of some hard ones. How hard is it to fix the grappa recon to write out the right number of frames? doug On 9/22/10 1:35 AM, r...@nmr.mgh.harvard.edu wrote: > Dear Free Surfers, > > I am analyzing fMRI time series that were reconstructed offline (GRAPPA > data that needed some artifact corrections, long story). Unfortunately, > the offline reconstructed f.nii do not include proper header info. I think > I was able to set the orientations correctly using mri_convert, but now > FSFAST preprocessing (specifically, mc-sess) fails because the headers say > that the number of TRs (number of full volume acquisitions) in the > measurement is 1, whereas in fact the correct value is 316. > > I could not find a tool that could change the "nframes" value (mri_convert > can adjust many other things but not this one it seems). Any suggestions? > > > Bests, > > Tommi > > > --- > Tommi Raij, M.D., Ph.D. > MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging > Bldg 149, 13th St > Charlestown, MA 02129 > U.S.A. > > ___ > 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.
Re: [Freesurfer] CSF volume
Hi Ed you would need a T2 or PD scan for that. The CSF label isn't reliable and only refers to bits of CSF here and there (not sure why the CMA included it at all) cheers Bruce On Wed, 22 Sep 2010, Ed Gronenschild wrote: > Hi, > > One of the volumes listed in the aseg.stats is > called "CSF". Its volume is too small to indicate > the total CSF volume of the brain. What is its > meaning? > > If I would like to get the total CSF volume how > should I proceed? > > Ed > > ___ > 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] CSF volume
Hi, One of the volumes listed in the aseg.stats is called "CSF". Its volume is too small to indicate the total CSF volume of the brain. What is its meaning? If I would like to get the total CSF volume how should I proceed? Ed ___ 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] preproc-sess failing
Hello freesurfers, I am trying to unpack a couple of recent subjects in Stable 4. I ran all steps through recon-all without error. However, when I try to run the next step, preproc-sess, it keeps failing. This is the command I enter: preproc-sess -s FB0011060AA -fwhm 5 It works for about 30 seconds, and then I get the following in return niiRead(): bad number of dimensions (0) in 013/tmp.mc-afni2.15211/outvol.nii.gz reading info from 013/f.nii... $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from 013/tmp.mc-afni2.15211/outvol.nii.gz... ERROR: converting output Invalid null command. ERROR: mc-sess failed the error for the other subject was slightly different: niiRead(): error reading from 013/tmp.mc-afni2.15452/outvol.nii.gz reading info from 012/f.nii... $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from 013/tmp.mc-afni2.15452/outvol.nii.gz... ERROR: Read 14, expected 64 ERROR: converting output Invalid null command. ERROR: mc-sess failed Any idea what might be going on? I've done these same steps many times for processing data and have not before received this error. Thanks! Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital ___ 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.
