[Freesurfer] Using caudate as a seed
Hi, Is there any way in FSFAST to use caudate as a seed for connectivity analysis? I was checking to see if it had a seg id for which I could run fc-seed-config, but it only had ids for caudate intensity abnormalities. Thank you! Best, Talia ___ 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] mris_preproc subject-volume mismatch
It worked with the register.dat files. Thank you! From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Wednesday, July 06, 2016 2:07 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_preproc subject-volume mismatch Ah, the problem is with using an lta with 5.3 mris_preproc. I've put version 6 mris_preproc here ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_preproc try that and see if it works. Alternatively, you could convert the lta files to register.dat files On 07/06/2016 02:02 PM, Raney, Talia L. wrote: > Hmm, it says that there is one frame in each of the subjects. > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve > [gr...@nmr.mgh.harvard.edu] > Sent: Wednesday, July 06, 2016 1:54 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] mris_preproc subject-volume mismatch > > It must be that one of the ces files has multiple frames. Try running > mri_info --nframes ces.nii.gz > on all of the ces files to see how many frames are in each > > On 07/06/2016 01:39 PM, Raney, Talia L. wrote: >> mris_preproc --target fsaverage --hemi lh --iv >> WADG77j/restingstate/fc.lh-entorhinal.space.lh/lh-entorhinal/ces.nii.gz >> WADG77j/restingstate/bb.register.lta --iv >> WADG77k/restingstate/fc.lh-entorhinal.space.lh/lh-entorhinal/ces.nii.gz >> WADG77k/restingstate/bb.register.lta --projfrac 0.5 --out lh.ces.mgh >> ERROR: number of input volumes (2) does not equal number of subjects (8) >> It apparently thinks one volume is 4 subjects but when checking >> bb.register.lta, it doesn't appear to be the case. >> Thanks! >> Talia >> >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve >> [gr...@nmr.mgh.harvard.edu] >> Sent: Wednesday, July 06, 2016 1:19 PM >> To: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] mris_preproc subject-volume mismatch >> >> can you send the terminal output? >> >> On 07/06/2016 11:32 AM, Raney, Talia L. wrote: >>> Hi FreeSurfer users, >>> I'm trying to use mri-preproc to do a group fMRI analysis(based on the >>> tutorial). However, I keep getting an error that the number of input >>> volumes does not equal number of subjects. It seems one volume is counted >>> as 4 subjects. I'm wondering what the command determines to be the subject >>> list when you use the --iv flag. >>> For reference, I'm basing it off of this command: >>> mris_preproc --target fsaverage --hemi lh \ >>> --iv fbirn-101/ces.nii fbirn-101/bb.register.lta \ >>> --iv fbirn-103/ces.nii fbirn-103/bb.register.lta \ >>> --iv fbirn-104/ces.nii fbirn-104/bb.register.lta \ >>> --iv fbirn-105/ces.nii fbirn-105/bb.register.lta \ >>> --iv fbirn-106/ces.nii fbirn-106/bb.register.lta \ >>> --projfrac 0.5 \ >>> --out lh.ces.mgh >>> Thanks! >>> Talia >>> ___ >>> 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: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> ___ >> 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 >> >> > -- > 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: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > >
Re: [Freesurfer] mris_preproc subject-volume mismatch
Hmm, it says that there is one frame in each of the subjects. From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Wednesday, July 06, 2016 1:54 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_preproc subject-volume mismatch It must be that one of the ces files has multiple frames. Try running mri_info --nframes ces.nii.gz on all of the ces files to see how many frames are in each On 07/06/2016 01:39 PM, Raney, Talia L. wrote: > mris_preproc --target fsaverage --hemi lh --iv > WADG77j/restingstate/fc.lh-entorhinal.space.lh/lh-entorhinal/ces.nii.gz > WADG77j/restingstate/bb.register.lta --iv > WADG77k/restingstate/fc.lh-entorhinal.space.lh/lh-entorhinal/ces.nii.gz > WADG77k/restingstate/bb.register.lta --projfrac 0.5 --out lh.ces.mgh > ERROR: number of input volumes (2) does not equal number of subjects (8) > It apparently thinks one volume is 4 subjects but when checking > bb.register.lta, it doesn't appear to be the case. > Thanks! > Talia > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve > [gr...@nmr.mgh.harvard.edu] > Sent: Wednesday, July 06, 2016 1:19 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] mris_preproc subject-volume mismatch > > can you send the terminal output? > > On 07/06/2016 11:32 AM, Raney, Talia L. wrote: >> Hi FreeSurfer users, >> I'm trying to use mri-preproc to do a group fMRI analysis(based on the >> tutorial). However, I keep getting an error that the number of input volumes >> does not equal number of subjects. It seems one volume is counted as 4 >> subjects. I'm wondering what the command determines to be the subject list >> when you use the --iv flag. >> For reference, I'm basing it off of this command: >> mris_preproc --target fsaverage --hemi lh \ >> --iv fbirn-101/ces.nii fbirn-101/bb.register.lta \ >> --iv fbirn-103/ces.nii fbirn-103/bb.register.lta \ >> --iv fbirn-104/ces.nii fbirn-104/bb.register.lta \ >> --iv fbirn-105/ces.nii fbirn-105/bb.register.lta \ >> --iv fbirn-106/ces.nii fbirn-106/bb.register.lta \ >> --projfrac 0.5 \ >> --out lh.ces.mgh >> Thanks! >> Talia >> ___ >> 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: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > ___ > 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 > > -- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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] mris_preproc subject-volume mismatch
mris_preproc --target fsaverage --hemi lh --iv WADG77j/restingstate/fc.lh-entorhinal.space.lh/lh-entorhinal/ces.nii.gz WADG77j/restingstate/bb.register.lta --iv WADG77k/restingstate/fc.lh-entorhinal.space.lh/lh-entorhinal/ces.nii.gz WADG77k/restingstate/bb.register.lta --projfrac 0.5 --out lh.ces.mgh ERROR: number of input volumes (2) does not equal number of subjects (8) It apparently thinks one volume is 4 subjects but when checking bb.register.lta, it doesn't appear to be the case. Thanks! Talia From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Wednesday, July 06, 2016 1:19 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_preproc subject-volume mismatch can you send the terminal output? On 07/06/2016 11:32 AM, Raney, Talia L. wrote: > Hi FreeSurfer users, > I'm trying to use mri-preproc to do a group fMRI analysis(based on the > tutorial). However, I keep getting an error that the number of input volumes > does not equal number of subjects. It seems one volume is counted as 4 > subjects. I'm wondering what the command determines to be the subject list > when you use the --iv flag. > For reference, I'm basing it off of this command: > mris_preproc --target fsaverage --hemi lh \ >--iv fbirn-101/ces.nii fbirn-101/bb.register.lta \ >--iv fbirn-103/ces.nii fbirn-103/bb.register.lta \ >--iv fbirn-104/ces.nii fbirn-104/bb.register.lta \ >--iv fbirn-105/ces.nii fbirn-105/bb.register.lta \ >--iv fbirn-106/ces.nii fbirn-106/bb.register.lta \ >--projfrac 0.5 \ >--out lh.ces.mgh > Thanks! > Talia > ___ > 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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] mris_preproc subject-volume mismatch
Hi FreeSurfer users, I'm trying to use mri-preproc to do a group fMRI analysis(based on the tutorial). However, I keep getting an error that the number of input volumes does not equal number of subjects. It seems one volume is counted as 4 subjects. I'm wondering what the command determines to be the subject list when you use the --iv flag. For reference, I'm basing it off of this command: mris_preproc --target fsaverage --hemi lh \ --iv fbirn-101/ces.nii fbirn-101/bb.register.lta \ --iv fbirn-103/ces.nii fbirn-103/bb.register.lta \ --iv fbirn-104/ces.nii fbirn-104/bb.register.lta \ --iv fbirn-105/ces.nii fbirn-105/bb.register.lta \ --iv fbirn-106/ces.nii fbirn-106/bb.register.lta \ --projfrac 0.5 \ --out lh.ces.mgh Thanks! Talia ___ 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] Found 0 unique series
gn/1/users/traney/Projects/FC-REVEAL-practice/DEMA65e/dcmunpack.log Found 0 unique series: echo "Subject $Patient" Patient: Undefined variable. It's just weird because it runs for most subjects but not a particular few. Thanks! Best, Talia From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Wednesday, June 15, 2016 4:43 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Found 0 unique series The problem appears to be cat: /imagelist.dat: No such file or directory Not sure what is going on there. Make sure you're not in / when running it or that the output points to /. Try running it with -debug as the first argument and sending the output. On 06/15/2016 04:36 PM, Raney, Talia L. wrote: > My command line is dcmunpack -src $dcmdir -targ $homedir/$subj -fsfast -run > $run_num restingstate nii.gz f.nii.gz and the output is > --- >1 24 restingstate f 0 0 > --- > Searching for matching files > Wed Jun 15 16:34:27 EDT 2016 > Wed Jun 15 16:34:27 EDT 2016 > Found 65 total files. > cat: /imagelist.dat: No such file or directory > Found 0 unique series: > Patient: Undefined variable. > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve > [gr...@nmr.mgh.harvard.edu] > Sent: Wednesday, June 15, 2016 4:08 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Found 0 unique series > > what is your command line and what is the full terminal output > > On 06/15/2016 04:06 PM, Raney, Talia L. wrote: >> Hi FreeSurfer users, >> I've been running dcmunpack and I get an error that said Found 0 unique >> series, even though it has dicom files. What does this mean and what could I >> do to fix the problem? >> Best, >> Talia >> ___ >> 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: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > ___ > 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 > > -- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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] Found 0 unique series
My command line is dcmunpack -src $dcmdir -targ $homedir/$subj -fsfast -run $run_num restingstate nii.gz f.nii.gz and the output is --- 1 24 restingstate f 0 0 --- Searching for matching files Wed Jun 15 16:34:27 EDT 2016 Wed Jun 15 16:34:27 EDT 2016 Found 65 total files. cat: /imagelist.dat: No such file or directory Found 0 unique series: Patient: Undefined variable. From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Wednesday, June 15, 2016 4:08 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Found 0 unique series what is your command line and what is the full terminal output On 06/15/2016 04:06 PM, Raney, Talia L. wrote: > Hi FreeSurfer users, > I've been running dcmunpack and I get an error that said Found 0 unique > series, even though it has dicom files. What does this mean and what could I > do to fix the problem? > Best, > Talia > ___ > 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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] Found 0 unique series
Hi FreeSurfer users, I've been running dcmunpack and I get an error that said Found 0 unique series, even though it has dicom files. What does this mean and what could I do to fix the problem? Best, Talia ___ 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] Selxavg3-sess with no-con-ok and ROI analyses
That's my bad. I tried with selxavg3-sess and I get a different error saying no contrasts and to create contrasts with mkcontrast-sess or run with -no-con-ok. Is it possible I did mkanalysis-sess wrong? Thanks! Talia From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Wednesday, June 01, 2016 5:21 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Selxavg3-sess with no-con-ok and ROI analyses Are you using selxavg-sess or selxavg3-sess. you should be using selxavg3-sess On 06/01/2016 03:45 PM, Raney, Talia L. wrote: > Okay, the thing is that when I remove the no-con flag I get this error > "ERROR: the design type of this analysis is notask >selxavg-sess can only be used to analyse event-related and blocked", which > means I have to change the analysis.info using mkanalysis-sess,correct? Which > flag would I use then? Does this mean then that I have to use the seed as a > task regressor? > Thank you! > Best, > Talia > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve > [gr...@nmr.mgh.harvard.edu] > Sent: Wednesday, June 01, 2016 2:42 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Selxavg3-sess with no-con-ok and ROI analyses > > Don't include the -no-con-ok flag. For resting state, you don't need to > run mkcontrast-sess because a contrast will automatically be created for > you. > > On 06/01/2016 02:24 PM, Raney, Talia L. wrote: >> Hi FreeSurfer users, >> I have some resting state data that I preprocessed and conducted first level >> analyses using the flag -no-con-ok. Since no ces.nii.gz or sig.nii.gz is >> createdcomes up because there is no contrast, I'm wondering if it's possible >> to conduct functional ROI analyses with the data processed this way. Or >> would I have to do ROI analyses with the data processed in a seed-based >> manner where the seed is the "contrast"? >> Best, >> Talia >> ___ >> 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: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > ___ > 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 > > -- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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] Selxavg3-sess with no-con-ok and ROI analyses
Okay, the thing is that when I remove the no-con flag I get this error "ERROR: the design type of this analysis is notask selxavg-sess can only be used to analyse event-related and blocked", which means I have to change the analysis.info using mkanalysis-sess,correct? Which flag would I use then? Does this mean then that I have to use the seed as a task regressor? Thank you! Best, Talia From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Wednesday, June 01, 2016 2:42 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Selxavg3-sess with no-con-ok and ROI analyses Don't include the -no-con-ok flag. For resting state, you don't need to run mkcontrast-sess because a contrast will automatically be created for you. On 06/01/2016 02:24 PM, Raney, Talia L. wrote: > Hi FreeSurfer users, > I have some resting state data that I preprocessed and conducted first level > analyses using the flag -no-con-ok. Since no ces.nii.gz or sig.nii.gz is > createdcomes up because there is no contrast, I'm wondering if it's possible > to conduct functional ROI analyses with the data processed this way. Or would > I have to do ROI analyses with the data processed in a seed-based manner > where the seed is the "contrast"? > Best, > Talia > ___ > 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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] Selxavg3-sess with no-con-ok and ROI analyses
Hi FreeSurfer users, I have some resting state data that I preprocessed and conducted first level analyses using the flag -no-con-ok. Since no ces.nii.gz or sig.nii.gz is createdcomes up because there is no contrast, I'm wondering if it's possible to conduct functional ROI analyses with the data processed this way. Or would I have to do ROI analyses with the data processed in a seed-based manner where the seed is the "contrast"? Best, Talia ___ 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] fcseed-sess ERROR: could not determine file for .../fmcpr
Hi Julio, You're right in that the problem is occurring in a later step. However, the fmcpr file is created during preprocessing. When you do the preprocessing step, it doesn't show an error occurring in the logs(this happened to me too because it said that preproc-sess was completed but fcseed-sess gave me this error that it could not determine the fmcpr file). You're right that you have to use the per-run parameter during preproc-sess. I think this will fix the problem if everything else is set up correctly. Best, Talia From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Julio Alberto González Torre [al099...@uji.es] Sent: Friday, April 15, 2016 11:42 AM To: Freesurfer support list Subject: Re: [Freesurfer] fcseed-sess ERROR: could not determine file for .../fmcpr Hi Talia. Thanks for the quick answer. But the preprocessing finished correctly without errors as I can check on all the log files generated in the same project folder. "subjectname" and $SUBJECTS_DIR are correctly placed. The problem is a later step (STEP 5, http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough), when I try to create FC seeds for an individual. As long as I can read in previously threads, the problem may be the parameter "-per-session", so now I'm trying to do it with "-per-run" parameter to check if the error remains. But I was unable to find a definitive fix for this error. 2016-04-15 14:09 GMT+02:00 Raney, Talia L. <tra...@partners.org<mailto:tra...@partners.org>>: Hi Julio, In the past I received this error because the subject was not preprocessed correctly. Make sure you have a link to the subject's structural recon folder in the resting state folder. In order to do this, you have to create a txt file(in this case it would 02_resting/subjectname) and within that txt file you put the name of the recon directory. After doing this, make sure that the $SUBJECTS_DIR is where the subject's recon folder is or else it won't fully run preprocessing. Hope this helps! Best, Talia From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> [freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of Julio Alberto González Torre [al099...@uji.es<mailto:al099...@uji.es>] Sent: Thursday, April 14, 2016 6:42 PM To: Freesurfer support list Subject: [Freesurfer] fcseed-sess ERROR: could not determine file for .../fmcpr Hi Freesurfer users. I am currently performing the steps of Functional Connectivity Walkthrough. And after resolving the problems in the first steps, specially in the preprocessing command (missing AFNI files), I'm now stuck in the 5th step: Creating the FC seeds for each subject. In the 4th step I've created the parameters for a region of interest. In this case, cheking the FreeSurferColorLUT.txt, I run this command to create the parameters for Left CA1 of Hippocampus (after the reconstruction, I performed the hippocampal subfields): fcseed-config -segid 552 -fcname L_CA1.dat -fsd rest -mean -cfg mean.L_CA1.config In the 5th step, when I run the fcseed-sess command, I obtain this error and I'm unable to figure out why: fcseed-sess -s con_algon -cfg L_CA1.config ERROR: could not determine file for /Users/acad1215inv/Desktop/ALBERTO/08_Conectividad/CONECTIVIDAD/02_resting/con_algon/rest/009/fmcpr stem2fname /Users/acad1215inv/Desktop/ALBERTO/08_Conectividad/CONECTIVIDAD/02_resting/con_algon/rest/009/fmcpr I've checked the "009" folder and there isn't any file with the name "fmcpr". Does someone have any idea how could I resolve this? Thanks! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto: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] DLPFC seed
Hi all, I'm trying to do FC connectivity analysis using the dorsalateral prefrontal cortex as a seed. I checked the text file $FREESURFER_HOME/average/colortable_desikan_killiany.txt and it looks like DLPFC is not listed as a possible structure to do the FC analysis. I attempted to use lh-prefrontal and rh-prefrontal but selxavg3-sess fails because there's no volume/label in fsaverage that is associated with it. Any suggestions on what seeds I could use? Would I have to combine or parcellate other existing seeds? Thank you! Best, Talia ___ 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.
