[Freesurfer] question about TRACULA
Dear Madam/Sir, I am trying to applying TRACULA on my data but when I run the following command: trac-all -prep -c /Users/Desktop/FreesurferData/SUBJECT1/dmrirc_subject1 after some processing I obtain the following error xfmrot /Users/luciabilleci/Desktop/FreesurferData/FRANCINI1/dmri/dwi.ecclog /Users/luciabilleci/Desktop/FreesurferData/FRANCINI1/dmri/bvecs.norot /Users/luciabilleci/Desktop/FreesurferData/FRANCINI1/dmri/bvecs printf: .97: expected numeric value printf: .002040: expected numeric value printf: .001230: expected numeric value printf: 8.010424: not completely converted printf: -4.983286: not completely converted printf: -.000389: expected numeric value printf: -.759652: expected numeric value printf: -5.031242: not completely converted printf: 8.006841: not completely converted printf: 7.864457: not completely converted printf: 3.131627: not completely converted printf: -3.216084: not completely converted printf: -1.957800: not completely converted printf: 7.048668: not completely converted printf: 5.956787: not completely converted printf: -7.998542: not completely converted printf: 1.996216: not completely converted printf: 4.004804: not completely converted printf: 7.008384: not completely converted printf: -2.985687: not completely converted printf: 3.996015: not completely converted printf: -.986002: expected numeric value printf: -9.000231: not completely converted printf: .153834: expected numeric value printf: 7.937660: not completely converted printf: .875656: expected numeric value printf: 4.150514: not completely converted printf: -2.115330: not completely converted printf: 8.962086: not completely converted printf: 2.050965: not completely converted printf: 5.758588: not completely converted printf: 8.092588: not completely converted printf: -4.165180: not completely converted printf: 4.753098: not completely converted printf: 5.079427: not completely converted printf: -6.132490: not completely converted printf: -4.21: not completely converted printf: 4.007709: not completely converted printf: 6.995579: not completely converted printf: -4.879465: not completely converted printf: -7.066532: not completely converted printf: 1.120257: not completely converted printf: -5.186508: not completely converted printf: -2.066011: not completely converted printf: -7.863320: not completely converted printf: -5.008038: not completely converted printf: 5.995846: not completely converted printf: 3.996178: not completely converted printf: 5.717007: not completely converted printf: 5.121524: not completely converted printf: -7.147437: not completely converted printf: 1.743757: not completely converted printf: 7.060581: not completely converted printf: -9.005971: not completely converted printf: -4.251174: not completely converted printf: 5.953915: not completely converted printf: -4.845450: not completely converted printf: -4.010977: not completely converted printf: -8.049025: not completely converted printf: -2.850488: not completely converted printf: 4.005690: not completely converted printf: -7.995851: not completely converted printf: 1.010371: not completely converted printf: -5.118400: not completely converted printf: -4.070279: not completely converted printf: -6.872761: not completely converted printf: 8.143535: not completely converted printf: 4.835332: not completely converted printf: 1.817269: not completely converted printf: 2.268035: not completely converted printf: -2.989943: not completely converted printf: 7.931980: not completely converted printf: -4.199139: not completely converted printf: -3.025800: not completely converted printf: -8.900100: not completely converted grep: /Users/luciabilleci/Desktop/FreesurferData/FRANCINI1/dmri/dcminfo.dat: No such file or directory fslroi /Users/luciabilleci/Desktop/FreesurferData/FRANCINI1/dmri/dwi.nii.gz /Users/luciabilleci/Desktop/FreesurferData/FRANCINI1/dmri/lowb.nii.gz 0 Usage: fslroi fslroi fslroi Note: indexing (in both time and space) starts with 0 not 1! Inputting -1 for a size will set it to the full image extent for that dimension. Could you please give me some help? Thanks a lot Best Regards Lucia Billeci_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ Dr. Lucia Billeci, PhD Institute of Clinical Physiology (IFC) National Research Council (CNR) via Moruzzi 1, 56124, Pisa ITALY Tel: +39-0506213204 e-mail: lucia.bill...@ifc.cnr.it _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ___ 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
[Freesurfer] Error running TRACULA
Dear all, I am trying to apply TRACULA on my DATA (GE data) but when I run the following command: trac-all -prep -c /Users/Desktop/FreesurferData/SUBJECT1/dmrirc_subject1 after eddy current correction, I obtain this error: mv -f /Users/luciabilleci/Desktop/FreesurferData/FRANCINI1/dmri/bvecs /Users/luciabilleci/Desktop/FreesurferData/FRANCINI1/dmri/bvecs.norot xfmrot /Users/luciabilleci/Desktop/FreesurferData/FRANCINI1/dmri/dwi.ecclog /Users/luciabilleci/Desktop/FreesurferData/FRANCINI1/dmri/bvecs.norot /Users/luciabilleci/Desktop/FreesurferData/FRANCINI1/dmri/bvecs printf: -.93: expected numeric value printf: -.003594: expected numeric value printf: .000852: expected numeric value R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. fslroi /Users/luciabilleci/Desktop/FreesurferData/FRANCINI1/dmri/dwi.nii.gz /Users/luciabilleci/Desktop/FreesurferData/FRANCINI1/dmri/lowb.nii.gz 0 Usage: fslroi fslroi fslroi Note: indexing (in both time and space) starts with 0 not 1! Inputting -1 for a size will set it to the full image extent for that dimension. Darwin dhcp225.ifc.cnr.it 11.4.2 Darwin Kernel Version 11.4.2: Thu Aug 23 16:25:48 PDT 2012; root:xnu-1699.32.7~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Gio 26 Set 2013 10:12:38 CEST I attach my bvals and bvecs Could you help me? Thanks Lucia bvals Description: Binary data bvecs 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.
Re: [Freesurfer] Error running TRACULA
Dear Anastasia, I added in the dmrirc file the following line: set nb0 = 1 because I red in the forum that it is necessary to indicate the number of b0 volume and I don't get the error about fslroi anymore. However now I have the following error: Error: bvecs and bvals don't have the same number of entries I removed the blank line as you suggested (see attach) so I don't understand the error Thanks Lucia bvals Description: Binary data bvecs Description: Binary data _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ Dr. Lucia Billeci, PhD Institute of Clinical Physiology (IFC) National Research Council (CNR) via Moruzzi 1, 56124, Pisa ITALY Tel: +39-0506213204 e-mail: lucia.bill...@ifc.cnr.it _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ Il giorno 26/set/2013, alle ore 18:31, Anastasia Yendiki ha scritto: > > Hi Lucia - Does it work if you remove the extra blank line at the end of the > bvecs file? > > a.y > > On Thu, 26 Sep 2013, Lucia Billeci wrote: > >> Dear all, >> >> I am trying to apply TRACULA on my DATA (GE data) but when I run the >> following command: >> >> trac-all -prep -c /Users/Desktop/FreesurferData/SUBJECT1/dmrirc_subject1 >> >> after eddy current correction, I obtain this error: >> >> mv -f /Users/luciabilleci/Desktop/FreesurferData/FRANCINI1/dmri/bvecs >> /Users/luciabilleci/Desktop/FreesurferData/FRANCINI1/dmri/bvecs.norot >> xfmrot /Users/luciabilleci/Desktop/FreesurferData/FRANCINI1/dmri/dwi.ecclog >> /Users/luciabilleci/Desktop/FreesurferData/FRANCINI1/dmri/bvecs.norot >> /Users/luciabilleci/Desktop/FreesurferData/FRANCINI1/dmri/bvecs >> printf: -.93: expected numeric value >> printf: -.003594: expected numeric value >> printf: .000852: expected numeric value >> R: Subscript out of range. >> R: Subscript out of range. >> R: Subscript out of range. >> fslroi /Users/luciabilleci/Desktop/FreesurferData/FRANCINI1/dmri/dwi.nii.gz >> /Users/luciabilleci/Desktop/FreesurferData/FRANCINI1/dmri/lowb.nii.gz 0 >> >> Usage: fslroi >> fslroi >> >> fslroi >> >> Note: indexing (in both time and space) starts with 0 not 1! Inputting -1 >> for a size will set it to the full image extent for that dimension. >> Darwin dhcp225.ifc.cnr.it 11.4.2 Darwin Kernel Version 11.4.2: Thu Aug 23 >> 16:25:48 PDT 2012; root:xnu-1699.32.7~1/RELEASE_X86_64 x86_64 >> >> trac-preproc exited with ERRORS at Gio 26 Set 2013 10:12:38 CEST >> >> I attach my bvals and bvecs >> Could you help me? >> >> Thanks >> Lucia >> >> >> >> >> >> > > > 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] Error running TRACULA
Hi Anastasia here are the files Thanks Lucia bvals Description: Binary data bvecs Description: Binary data _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ Dr. Lucia Billeci, PhD Institute of Clinical Physiology (IFC) National Research Council (CNR) via Moruzzi 1, 56124, Pisa ITALY Tel: +39-0506213204 e-mail: lucia.bill...@ifc.cnr.it _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ Il giorno 27/set/2013, alle ore 17:06, Anastasia Yendiki ha scritto: > > Hi Lucia - The nb0 thing isn't used any more, it was in the old version of > tracula only (the one in freesurfer 5.1). > > Can you send the version of the bvecs and bvals files that are in the dmri/ > directory? > > Thanks, > a.y > > On Fri, 27 Sep 2013, Lucia Billeci wrote: > >> Dear Anastasia, >> >> I added in the dmrirc file the following line: >> >> set nb0 = 1 >> >> because I red in the forum that it is necessary to indicate the number of b0 >> volume and I don't get the error about fslroi anymore. However now I have >> the following error: >> >> Error: bvecs and bvals don't have the same number of entries >> >> >> I removed the blank line as you suggested (see attach) so I don't understand >> the error >> >> >> Thanks >> Lucia >> >> > > > 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] Error running TRACULA
Dear Anastasia, using the command you told me I solved the problem with the bvecs file, however I get this error dmri_train(8994) malloc: *** mmap(size=159744) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRIalloc(218, 182, 182): could not allocate 158704 bytes for 14th slice Cannot allocate memory Darwin dhcp-71-112.ifc.cnr.it 11.4.2 Darwin Kernel Version 11.4.2: Thu Aug 23 16:25:48 PDT 2012; root:xnu-1699.32.7~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Wed Oct 2 10:04:53 CEST 2013 Is it a memory problem? Do I need to change memory allocation? Thanks again. Lucia _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ Dr. Lucia Billeci, PhD Institute of Clinical Physiology (IFC) National Research Council (CNR) via Moruzzi 1, 56124, Pisa ITALY Tel: +39-0506213204 e-mail: lucia.bill...@ifc.cnr.it _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ Il giorno 27/set/2013, alle ore 18:08, Anastasia Yendiki ha scritto: > > Hi Lucia - The bvecs file is full of "0,000". I'm guessing the problem is > that your environment is set to use the comma instead of the point as the > decimal separator. Can you try this and then rerun? > > setenv LANG en_US.UTF-8 > > Hope this helps, > a.y > > On Fri, 27 Sep 2013, Lucia Billeci wrote: > >> Hi Anastasia >> >> here are the files >> >> Thanks >> Lucia >> >> >> >> > > > 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] Fwd: Error running TRACULA
Thanks a lot Anastasia for your help. I will install the new version and run it on my data. Best wishes Lucia Inizio messaggio inoltrato: > Da: Anastasia Yendiki > Oggetto: Re: [Freesurfer] Error running TRACULA > Data: 02 ottobre 2013 17:23:42 GMT+02:00 > A: Lucia Billeci > Cc: freesurfer@nmr.mgh.harvard.edu > > > Hi Lucia - You are using an older version of tracula (from freesurfer 5.1 > instead of 5.3). This version used to have memory issues in the mac build. > There is an update of the 5.1 mac build that addresses the memory issue, but > since you are just starting out, I *highly* recommend to use the 5.3 version. > It has improved both speed and performance. All this info is here: > http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula/#Updates > > Also, please make sure to send these messages to the freesuerfer list and not > just to me personally. This way the messages are archived, which reduces the > replication of questions. > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/ > > Thanks! > a.y > > On Wed, 2 Oct 2013, Lucia Billeci wrote: > >> I found this: >> build-stamp.txt: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 >> Lucia >> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ >> Dr. Lucia Billeci, PhD >> Institute of Clinical Physiology (IFC) >> National Research Council (CNR) >> via Moruzzi 1, 56124, Pisa >> ITALY >> Tel: +39-0506213204 >> e-mail: lucia.bill...@ifc.cnr.it >> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ >> Il giorno 02/ott/2013, alle ore 16:38, Anastasia Yendiki ha scritto: >> >> build-stamp >> > > > 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] TRACULA statistics
Dear all, I noticed that in the TRACULA statistics output files (pathstats.overall.txt) the variable "Count" that should indicate the number of sample paths in the WM tract is the same for all the computed tract. Could anyone tell me why this happen? Thanks a lot Regards Lucia _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ Dr. Lucia Billeci, PhD Institute of Clinical Physiology (IFC) National Research Council (CNR) via Moruzzi 1, 56124, Pisa ITALY Tel: +39-0506213204 e-mail: lucia.bill...@ifc.cnr.it _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ___ 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] TRACULA statistics
Hi Anastasia, thanks for you answer. Now I have understood the meaning of that parameter. Best regards Lucia On Oct 14, 2013, at 10:58 PM, Anastasia Yendiki wrote: > > Hi Lucia - It's how many sample paths were drawn to produce the probability > distribution of the path (path.pd.nii.gz). It depends on the configuration > parameters (nsample, nkeep), so it'll be the same if these configuration > parameters are the same. > > Hope this helps, > a.y > > On Mon, 14 Oct 2013, Lucia Billeci wrote: > >> Dear all, >> I noticed that in the TRACULA statistics output files >> (pathstats.overall.txt) the variable "Count" that >> should indicate the number of sample paths in the WM tract is the same for >> all the computed tract. Could >> anyone tell me why this happen? >> Thanks a lot >> Regards >> Lucia >> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ >> Dr. Lucia Billeci, PhD >> Institute of Clinical Physiology (IFC) >> National Research Council (CNR) >> via Moruzzi 1, 56124, Pisa >> ITALY >> Tel: +39-0506213204 >> e-mail: lucia.bill...@ifc.cnr.it >> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ >> > > > 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. Dr. Lucia Billeci, PhD, Engineer National Research Council of Italy (CNR) Institute of Clinical Physiology (IFC) via Moruzzi, 1 Pisa - Italy http://www.ifc.cnr.it Tel. +39-050-3152182 Cell. +39-339-1863902 Email: lucia.bill...@ifc.cnr.it ___ 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] TRACULA statistics
Dear Anastasia and all, how can I understand which are the region of the brain in which the brain base been parecellated that each tract generated by TRACULA connect? For example if I look at the left uncinate fascicles how can I know which are the ROIs of the statistical output from the cortical parcellation that it connects? Thanks Lucia On Oct 14, 2013, at 11:08 PM, Lucia Billeci wrote: > Hi Anastasia, > > thanks for you answer. Now I have understood the meaning of that parameter. > > Best regards > Lucia > > > On Oct 14, 2013, at 10:58 PM, Anastasia Yendiki wrote: > >> >> Hi Lucia - It's how many sample paths were drawn to produce the probability >> distribution of the path (path.pd.nii.gz). It depends on the configuration >> parameters (nsample, nkeep), so it'll be the same if these configuration >> parameters are the same. >> >> Hope this helps, >> a.y >> >> On Mon, 14 Oct 2013, Lucia Billeci wrote: >> >>> Dear all, >>> I noticed that in the TRACULA statistics output files >>> (pathstats.overall.txt) the variable "Count" that >>> should indicate the number of sample paths in the WM tract is the same for >>> all the computed tract. Could >>> anyone tell me why this happen? >>> Thanks a lot >>> Regards >>> Lucia >>> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ >>> Dr. Lucia Billeci, PhD >>> Institute of Clinical Physiology (IFC) >>> National Research Council (CNR) >>> via Moruzzi 1, 56124, Pisa >>> ITALY >>> Tel: +39-0506213204 >>> e-mail: lucia.bill...@ifc.cnr.it >>> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ >>> >> >> >> 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. > > Dr. Lucia Billeci, PhD, Engineer > National Research Council of Italy (CNR) > Institute of Clinical Physiology (IFC) > via Moruzzi, 1 Pisa - Italy > http://www.ifc.cnr.it > Tel. +39-050-3152182 Cell. +39-339-1863902 > Email: lucia.bill...@ifc.cnr.it > > > > > ___ > 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. Dr. Lucia Billeci, PhD, Engineer National Research Council of Italy (CNR) Institute of Clinical Physiology (IFC) via Moruzzi, 1 Pisa - Italy http://www.ifc.cnr.it Tel. +39-050-3152182 Cell. +39-339-1863902 Email: lucia.bill...@ifc.cnr.it ___ 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] TRACULA statistics
Thanks Anastasia, this is useful for visualization. But to construct a table with for each tracts the parcellation regions that it connects do I need to look at the image? Lucia On Oct 18, 2013, at 3:48 PM, Anastasia Yendiki wrote: > > Hi Lucia - You can look at the tracula output over the cortical parcellation > and subcortical segmentation in the individual's diffusion space like this: > > freeview dmri/dtifit_FA.nii.gz > dlabel/diff/aparc+aseg.bbr.nii.gz:colormap=lut:opacity=.5 -tv > dpath/merged_avg33_mni_bbr.mgz > > Hope this helps, > a.y > > On Fri, 18 Oct 2013, Lucia Billeci wrote: > >> Dear Anastasia and all, >> how can I understand which are the region of the brain in which the brain >> base been parecellated that each tract generated by TRACULA connect? >> For example if I look at the left uncinate fascicles how can I know which >> are the ROIs of the statistical output from the cortical parcellation that >> it connects? >> Thanks >> Lucia >> On Oct 14, 2013, at 11:08 PM, Lucia Billeci wrote: >> >> Hi Anastasia, >> thanks for you answer. Now I have understood the meaning of that >> parameter. >> Best regards >> Lucia >> On Oct 14, 2013, at 10:58 PM, Anastasia Yendiki wrote: >> >> Hi Lucia - It's how many sample paths were drawn to >> produce the probability distribution of the path >> (path.pd.nii.gz). It depends on the configuration >> parameters (nsample, nkeep), so it'll be the same if these >> configuration parameters are the same. >> >> Hope this helps, >> a.y >> >> On Mon, 14 Oct 2013, Lucia Billeci wrote: >> >>Dear all, >> >>I noticed that in the TRACULA statistics >>output files (pathstats.overall.txt) the >>variable "Count" that >> >>should indicate the number of sample paths in >>the WM tract is the same for all the computed >>tract. Could >> >>anyone tell me why this happen? >> >>Thanks a lot >> >>Regards >> >>Lucia >> >>_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ >> >>Dr. Lucia Billeci, PhD >> >>Institute of Clinical Physiology (IFC) >> >>National Research Council (CNR) >> >>via Moruzzi 1, 56124, Pisa >> >>ITALY >> >>Tel: +39-0506213204 >> >>e-mail: lucia.bill...@ifc.cnr.it >> >>_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ >> >> 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. >> Dr. Lucia Billeci, PhD, Engineer >> National Research Council of Italy (CNR) >> Institute of Clinical Physiology (IFC) >> via Moruzzi, 1 Pisa - Italy >> http://www.ifc.cnr.it >> Tel. +39-050-3152182 Cell. +39-339-1863902 >> Email: lucia.bill...@ifc.cnr.it >> ___ >> 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. >> Dr. Lucia Billeci, PhD, Engineer >> National Research Council of Italy (CNR) >> Institute of Clinical Physiology (IFC) >> via Moruzzi, 1 Pisa - Italy >> http://www.ifc.cnr.it >> Tel. +39-050-3152182 Cell. +39-339-1863902 >> Email: lucia.bill...@ifc.cnr.it Dr. Lucia Billeci, PhD, Engineer National Research Council of Italy (CNR) Institute of Clinical Physiology (IFC) via Moruzzi, 1 Pisa - Italy http://www.ifc.cnr.it Tel. +39-050-3152182 Cell. +39-339-1863902 Email: lucia.bill...@ifc.cnr.it ___ 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] TRACULA statistics
Dear Anastasia, I tried the command you suggested me and i obtained the output I attach to the mail. I would like to ask you if I understood well shot it means. In this case left uncinatus connects the following cortex areas: ctx-lh-fusiform ctx-lh-inferiortemporal ctx-lh-lateralorbitofrontal ctx-lh-medialorbitofrontal ctx-lh-middletemporal ctx-lh-rostralanteriorcingulate ctx-lh-superiortemporal ctx-lh-temporalpole ctx-lh-insula and for each area I have the volume of the path. Is it correct? Thanks Lucia _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ Dr. Lucia Billeci, PhD Institute of Clinical Physiology (IFC) National Research Council (CNR) via Moruzzi 1, 56124, Pisa ITALY Tel: +39-0506213204 e-mail: lucia.bill...@ifc.cnr.it _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ Il giorno 18/ott/2013, alle ore 17:32, Anastasia Yendiki ha scritto: > > Hi Lucia - You can probably do that with mri_segstats. Try something like: > > mri_segstats --seg dlabel/diff/aparc+aseg.bbr.nii.gz --ctab > $FREESURFER_HOME/FreeSurferColorLUT.txt --excludeid 0 --sum output.txt --i > dpath/lh.unc_AS_avg32_mni_flt/path.pd.nii.gz > > And similarly for any other pathway. See the mri_segstats help for more usage > info. Let me know if this gives you what you need. > > a.y > > On Fri, 18 Oct 2013, Lucia Billeci wrote: > >> Thanks Anastasia, this is useful for visualization. But to construct a table >> with for each tracts the parcellation regions that it connects do I need to >> look at the image? >> Lucia >> On Oct 18, 2013, at 3:48 PM, Anastasia Yendiki wrote: >> >> Hi Lucia - You can look at the tracula output over the cortical >> parcellation and subcortical segmentation in the individual's >> diffusion space like this: >> >> freeview dmri/dtifit_FA.nii.gz >> dlabel/diff/aparc+aseg.bbr.nii.gz:colormap=lut:opacity=.5 -tv >> dpath/merged_avg33_mni_bbr.mgz >> >> Hope this helps, >> a.y >> >> On Fri, 18 Oct 2013, Lucia Billeci wrote: >> >>Dear Anastasia and all, >> >>how can I understand which are the region of the >>brain in which the brain >> >>base been parecellated that each tract generated by >>TRACULA connect? >> >>For example if I look at the left uncinate >>fascicles how can I know which >> >> are the ROIs of the statistical output from the >>cortical parcellation that >> >>it connects? >> >>Thanks >> >>Lucia >> >>On Oct 14, 2013, at 11:08 PM, Lucia Billeci wrote: >> >> Hi Anastasia, >> >>thanks for you answer. Now I have understood the >>meaning of that >> >>parameter. >> >>Best regards >> >>Lucia >> >>On Oct 14, 2013, at 10:58 PM, Anastasia Yendiki >>wrote: >> >> Hi Lucia - It's how many sample paths were >>drawn to >> >> produce the probability distribution of the >>path >> >> (path.pd.nii.gz). It depends on the >>configuration >> >> parameters (nsample, nkeep), so it'll be the >>same if these >> >> configuration parameters are the same. >> >> Hope this helps, >> >> a.y >> >> On Mon, 14 Oct 2013, Lucia Billeci wrote: >> >> Dear all, >> >> I noticed that in the TRACULA statistics >> >> output files (pathstats.overall.txt) the >> >> variable "Count" that >> >> should indicate the number of sample >>paths in >> >> the WM tract is the same for all the >>computed >> >> tract. Could >> >> anyone tell me why this happen? >> >> Thanks a lot >> >> Regards >> >> Lucia >> >> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ >>_ >> >> Dr. Lucia Billeci, PhD >> >> Institute of Clinic
Re: [Freesurfer] TRACULA statistics
0. 0. 0. 0. 0. 107 203266 1782.0 ctx-rh-frontalpole 0. 0. 0. 0. 0. 108 203377 2079.0 ctx-rh-temporalpole0. 0. 0. 0. 0. 109 203432 864.0 ctx-rh-transversetemporal 0. 0. 0. 0. 0. 110 2035 238 6426.0 ctx-rh-insula 0. 0. 0. 0. 0. _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _Dr. Lucia Billeci, PhDInstitute of Clinical Physiology (IFC)National Research Council (CNR)via Moruzzi 1, 56124, PisaITALYTel: +39-0506213204e-mail: lucia.bill...@ifc.cnr.it_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ Il giorno 18/ott/2013, alle ore 17:32, Anastasia Yendiki ha scritto:Hi Lucia - You can probably do that with mri_segstats. Try something like:mri_segstats --seg dlabel/diff/aparc+aseg.bbr.nii.gz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --excludeid 0 --sum output.txt --i dpath/lh.unc_AS_avg32_mni_flt/path.pd.nii.gzAnd similarly for any other pathway. See the mri_segstats help for more usage info. Let me know if this gives you what you need.a.yOn Fri, 18 Oct 2013, Lucia Billeci wrote:Thanks Anastasia, this is useful for visualization. But to construct a tablewith for each tracts the parcellation regions that it connects do I need tolook at the image?LuciaOn Oct 18, 2013, at 3:48 PM, Anastasia Yendiki wrote: Hi Lucia - You can look at the tracula output over the cortical parcellation and subcortical segmentation in the individual's diffusion space like this: freeview dmri/dtifit_FA.nii.gz dlabel/diff/aparc+aseg.bbr.nii.gz:colormap=lut:opacity=.5 -tv dpath/merged_avg33_mni_bbr.mgz Hope this helps, a.y On Fri, 18 Oct 2013, Lucia Billeci wrote: Dear Anastasia and all, how can I understand which are the region of the brain in which the brain base been parecellated that each tract generated by TRACULA connect? For example if I look at the left uncinate fascicles how can I know which are the ROIs of the statistical output from the cortical parcellation that it connects? Thanks Lucia On Oct 14, 2013, at 11:08 PM, Lucia Billeci wrote: Hi Anastasia, thanks for you answer. Now I have understood the meaning of that parameter. Best regards Lucia On Oct 14, 2013, at 10:58 PM, Anastasia Yendiki wrote: Hi Lucia - It's how many sample paths were drawn to produce the probability distribution of the path (path.pd.nii.gz). It depends on the configuration parameters (nsample, nkeep), so it'll be the same if these configuration parameters are the same. Hope this helps, a.y On Mon, 14 Oct 2013, Lucia Billeci wrote: Dear all, I noticed that in the TRACULA statistics output files (pathstats.overall.txt) the variable "Count" that should indicate the number of sample paths in the WM tract is the same for all the computed tract. Could anyone tell me why this happen? Thanks a lot Regards Lucia _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ Dr. Lucia Billeci, PhD Institute of Clinical Physiology (IFC) National Research Council (CNR) via Moruzzi 1, 56124, Pisa ITALY Tel: +39-0506213204 e-mail: lucia.bill...@ifc.cnr.it _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 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. Dr. Lucia Billeci, PhD, Engineer National Research Council of Italy (CNR)
[Freesurfer] problem using mri_vol2label for subcortical regions
External Email - Use Caution Dear Freesurfer Experts, I want to use mri_vol2label to obtain labels for subcortical regions. I tried the following command: mri_vol2label --c $SUBJECTS_DIR/fsaverage/mri/aseg.mgz --id 8 --l ./tests_label/8.label However I get the same vertex index for all the row, equal to -1: -1 -14.000 -92.000 -31.000 0.00 -1 -17.000 -92.000 -31.000 0.00 -1 -18.000 -92.000 -31.000 0.00 This happens for all the regions I selected. I have also tried adding the option —surf, as you suggested in previous posts: mri_vol2label --c $SUBJECTS_DIR/fsaverage/mri/aseg.mgz --id 8 --l ./tests_label/8.label --surf fsaverage lh white But I have the following error message: ERROR: dim mismatch between surface (163842) and input (16777216) Could you please help me? Thanks a lot in advance Best regards Lucia Billeci _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ Dr. Lucia Billeci, PhD Institute of Clinical Physiology (IFC) National Research Council (CNR) via Moruzzi 1, 56124, Pisa, Italy e-mail: lucia.bill...@ifc.cnr.it _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ___ 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] problem using mri_vol2label for subcortical regions
External Email - Use Caution Dear Brouce, thanks again. I would like exactly how to set mri_vol2label for subcortical regions as the way I used give me all the values of the first column equal to -1. This is a problem when I want to obtain obtain the centroid of the ROI using mri_surfcluster as I get an empty file. Hope Doug can help me. Thanks Lucia _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ Dr. Lucia Billeci, PhD Institute of Clinical Physiology (IFC) National Research Council (CNR) via Moruzzi 1, 56124, Pisa, Italy e-mail: lucia.bill...@ifc.cnr.it _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > On 2 May 2018, at 16:01, Bruce Fischl wrote: > > Hi Lucia > > can you cc the list so others can answer? You can't get a surface-based label > for a subcortical region as they aren't on (or close) to the surrface. I > think mri_vol2label is the right binary to create a volumetric ROI for each > one, but Doug will know > cheers > Bruce > > On Wed, 2 May 2018, Lucia Billeci wrote: > >> External Email - Use Caution >> Dear Bruce, >> thanks for your answer. >> I would like to obtain .label file for each subcortical region. I have >> tried the commands I >> reported in the previous messages but probably they are not correct. Could >> you please indicate me >> the correct way to have the .label file for subcortical regions? I am not >> sure if >> using mri_vol2label is the right way or maybe there is another strategy. >> Thanks >> regards >> Lucia >> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ >> Dr. Lucia Billeci, PhD >> Institute of Clinical Physiology (IFC) National Research Council (CNR) >> via Moruzzi 1, 56124, Pisa, Italy >> e-mail: lucia.bill...@ifc.cnr.it >> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ >> > > > 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] problem using mri_vol2label for subcortical regions
External Email - Use Caution Dear Bruce, the ROI appears correct in freeview. However I have a problem in the following step, i.e. obtain the centroid of the ROi. I used the following command: mri_surfcluster --in /Applications/freesurfer/subjects/fsaverage/surf/lh.thickness --clabel ./tests_label/sub/lh.amygdala.label --sum ./tests_label/sum/sum.lh.amygdala --centroid --thmin 0 --hemi lh --subject fsaverage —nofixmni However it doesn’t work for subcortical label files (it works with cortical ones). I have the following output and the command doesn’t produce the file sum.lh.amygdala: thsign = abs, id = 0 version $Id: mri_surfcluster.c,v 1.57.2.3 2016/11/17 18:19:42 zkaufman Exp $ hemi = lh srcid = /Applications/freesurfer/subjects/fsaverage/surf/lh.thickness srcsubjid = fsaverage srcsurf= white srcframe = 0 thsign = abs thmin = 0 thmax = -1 fdr= -1 minarea= 0 xfmfile= talairach.xfm clabelfile = ./tests_label/sub/lh.amygdala.label clabelinv = 0 nth = -1 sumfile = ./tests_label/sum/sum.lh.amygdala subjectsdir= /Applications/freesurfer/subjects FixMNI = 0 Loading clabel ./tests_label/sub/lh.amygdala.label. Found 1941 points in clabel. - XFM matrix (RAS2RAS) --- /Applications/freesurfer/subjects/fsaverage/mri/transforms/talairach.xfm 1.0 0.0 0.0 0.0; 0.0 1.0 0.0 0.0; 0.0 0.0 1.0 0.0; 0.0 0.0 0.0 1.0; Reading source surface /Applications/freesurfer/subjects/fsaverage/surf/lh.white Done reading source surface Computing metric properties Loading source values /Applications/freesurfer/bin/mri_surfcluster: line 3: 2828 Bus error: 10 mri_surfcluster.bin "$@" Maybe because lh.thickness is only for cortical regions? In this case, how can I obtain centroids of subcortical ROIs? Thanks Regards Lucia _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ Dr. Lucia Billeci, PhD Institute of Clinical Physiology (IFC) National Research Council (CNR) via Moruzzi 1, 56124, Pisa, Italy e-mail: lucia.bill...@ifc.cnr.it _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > On 2 May 2018, at 17:05, Bruce Fischl wrote: > > Hi Lucia > > the first column being -1 means that it is not mapped to the surface, so is > correct in your (subcortical) case. Try loading the label as an ROI in > freeview and see if it is correct > > cheers > Bruce > On Wed, 2 May 2018, Lucia Billeci wrote: > >> External Email - Use Caution >> Dear Brouce, >> thanks again. >> I would like exactly how to set mri_vol2label for subcortical regions as the >> way I used >> give me all the values of the first column equal to -1. This is a problem >> when I want >> to obtain obtain the centroid of the ROI using mri_surfcluster as I get an >> empty file. >> Hope Doug can help me. >> Thanks >> Lucia >> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ >> Dr. Lucia Billeci, PhD >> Institute of Clinical Physiology (IFC) National Research Council (CNR) >> via Moruzzi 1, 56124, Pisa, Italy >> e-mail: lucia.bill...@ifc.cnr.it >> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ >> >> On 2 May 2018, at 16:01, Bruce Fischl >> wrote: >> Hi Lucia >> can you cc the list so others can answer? You can't get a surface-based >> label for >> a subcortical region as they aren't on (or close) to the surrface. I think >> mri_vol2label is the right binary to create a volumetric ROI for each one, >> but >> Doug will know >> cheers >> Bruce >> On Wed, 2 May 2018, Lucia Billeci wrote: >> >> External Email - Use Caution >> Dear Bruce, >> thanks for your answer. >> I would like to obtain .label file for each subcortical region. I >> have tried the commands I >> reported in the previous messages but probably they are not correct. >> Could you please indicate me >> the correct way to have the .label file for subcortical regions? I am >> not sure if >> using mri_vol2label is the right way or maybe there is another >> strategy. >> Thanks >> regards >> Lucia >> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ >> Dr. Lucia Billeci, PhD >> Institute of Clinical Physiology (IFC) National Research Council >> (CNR) >> via Moruzzi 1, 56124, Pisa, Italy >> e-mail: lucia.bill...@ifc.cnr.it >> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ >> The information in this e-m
Re: [Freesurfer] problem using mri_vol2label for subcortical regions
External Email - Use Caution Dear Douglas, thanks a lot. This can solve my problem. Could you please give my some explanations about how to open and use the tool? Thanks Regards Lucia _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ Dr. Lucia Billeci, PhD Institute of Clinical Physiology (IFC) National Research Council (CNR) via Moruzzi 1, 56124, Pisa, Italy e-mail: lucia.bill...@ifc.cnr.it _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ___ 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] problem using mri_vol2label for subcortical regions
External Email - Use Caution Sorry Douglas, hereafter you can find previous emails Regards Lucia Dear Douglas, thanks a lot. This can solve my problem. Could you please give my some explanations about how to open and use the tool? Thanks Regards Lucia mri_surfcluster only works for surfaces (that's what the "surf" in the name means). If you want the centroid of a volume ROI use https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_segcentroids <https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_segcentroids> Dear Bruce, the ROI appears correct in freeview. However I have a problem in the following step, i.e. obtain the centroid of the ROi. I used the following command: mri_surfcluster --in /Applications/freesurfer/subjects/fsaverage/surf/lh.thickness --clabel ./tests_label/sub/lh.amygdala.label --sum ./tests_label/sum/sum.lh.amygdala --centroid --thmin 0 --hemi lh --subject fsaverage —nofixmni However it doesn’t work for subcortical label files (it works with cortical ones). I have the following output and the command doesn’t produce the file sum.lh.amygdala: thsign = abs, id = 0 version $Id: mri_surfcluster.c,v 1.57.2.3 2016/11/17 18:19:42 zkaufman Exp $ hemi = lh srcid = /Applications/freesurfer/subjects/fsaverage/surf/lh.thickness srcsubjid = fsaverage srcsurf= white srcframe = 0 thsign = abs thmin = 0 thmax = -1 fdr= -1 minarea= 0 xfmfile= talairach.xfm clabelfile = ./tests_label/sub/lh.amygdala.label clabelinv = 0 nth = -1 sumfile = ./tests_label/sum/sum.lh.amygdala subjectsdir= /Applications/freesurfer/subjects FixMNI = 0 Loading clabel ./tests_label/sub/lh.amygdala.label. Found 1941 points in clabel. - XFM matrix (RAS2RAS) --- /Applications/freesurfer/subjects/fsaverage/mri/transforms/talairach.xfm 1.0 0.0 0.0 0.0; 0.0 1.0 0.0 0.0; 0.0 0.0 1.0 0.0; 0.0 0.0 0.0 1.0; Reading source surface /Applications/freesurfer/subjects/fsaverage/surf/lh.white Done reading source surface Computing metric properties Loading source values /Applications/freesurfer/bin/mri_surfcluster: line 3: 2828 Bus error: 10 mri_surfcluster.bin "$@" Maybe because lh.thickness is only for cortical regions? In this case, how can I obtain centroids of subcortical ROIs? Thanks Regards Lucia Hi Lucia the first column being -1 means that it is not mapped to the surface, so is correct in your (subcortical) case. Try loading the label as an ROI in freeview and see if it is correct cheers Bruce Hi Lucia the first column being -1 means that it is not mapped to the surface, so is correct in your (subcortical) case. Try loading the label as an ROI in freeview and see if it is correct cheers Bruce Dear Brouce, thanks again. I would like exactly how to set mri_vol2label for subcortical regions as the way I used give me all the values of the first column equal to -1. This is a problem when I want to obtain obtain the centroid of the ROI using mri_surfcluster as I get an empty file. Hope Doug can help me. Thanks Lucia Hi Lucia can you cc the list so others can answer? You can't get a surface-based label for a subcortical region as they aren't on (or close) to the surrface. I think mri_vol2label is the right binary to create a volumetric ROI for each one, but Doug will know cheers Bruce Dear Freesurfer Experts, I want to use mri_vol2label to obtain labels for subcortical regions. I tried the following command: mri_vol2label --c $SUBJECTS_DIR/fsaverage/mri/aseg.mgz --id 8 --l ./tests_label/8.label However I get the same vertex index for all the row, equal to -1: -1 -14.000 -92.000 -31.000 0.00 -1 -17.000 -92.000 -31.000 0.00 -1 -18.000 -92.000 -31.000 0.00 This happens for all the regions I selected. I have also tried adding the option —surf, as you suggested in previous posts: mri_vol2label --c $SUBJECTS_DIR/fsaverage/mri/aseg.mgz --id 8 --l ./tests_label/8.label --surf fsaverage lh white But I have the following error message: ERROR: dim mismatch between surface (163842) and input (16777216) Could you please help me? Thanks a lot in advance Best regards Lucia Billeci _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ Dr. Lucia Billeci, PhD Institute of Clinical Physiology (IFC) National Research Council (CNR) via Moruzzi 1, 56124, Pisa, Italy e-mail: lucia.bill...@ifc.cnr.it _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > On 3 May 2018, at 17:53, Douglas N. Greve wrote: > > Please include previous emails so that I know what you are asking about. I > get a lot of emails:) > > > On 05/03/2018 05:07 AM, Lucia Billeci wrote: >> >> >> Dear D
Re: [Freesurfer] problem using mri_vol2label for subcortical regions
External Email - Use Caution Thank you. However I don’t know how to open the file .dms you sent me. I have tried several ways but unsuccessfully. Could you please tell me how to open files with this extension or maybe send me the file with another extension? Best regards Lucia _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ Dr. Lucia Billeci, PhD Institute of Clinical Physiology (IFC) National Research Council (CNR) via Moruzzi 1, 56124, Pisa, Italy e-mail: lucia.bill...@ifc.cnr.it _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > On 7 May 2018, at 19:32, Douglas N. Greve wrote: > > Something like > > mri_segcentroid --i aseg.mgz --o centroids.dat --ctab-default > > > On 05/05/2018 01:06 PM, Lucia Billeci wrote: >> >> Sorry Douglas, >> >> hereafter you can find previous emails >> >> Regards >> Lucia >> >> >> >> >> >> >> >> Dear Douglas, >> thanks a lot. This can solve my problem. Could you please give my some >> explanations about how to open and use the tool? >> >> Thanks >> Regards >> Lucia >> >> >> >> >> mri_surfcluster only works for surfaces (that's what the "surf" in the >> name means). If you want the centroid of a volume ROI use >> https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_segcentroids >> >> >> >> >> Dear Bruce, >> >> the ROI appears correct in freeview. However I have a problem in the >> following step, i.e. obtain the centroid of the ROi. >> >> I used the following command: >> >> mri_surfcluster --in >> /Applications/freesurfer/subjects/fsaverage/surf/lh.thickness --clabel >> ./tests_label/sub/lh.amygdala.label --sum ./tests_label/sum/sum.lh.amygdala >> --centroid --thmin 0 --hemi lh --subject fsaverage —nofixmni >> >> However it doesn’t work for subcortical label files (it works with cortical >> ones). I have the following output and the command doesn’t produce the file >> sum.lh.amygdala: >> >> thsign = abs, id = 0 >> version $Id: mri_surfcluster.c,v 1.57.2.3 2016/11/17 18:19:42 zkaufman Exp $ >> hemi = lh >> srcid = >> /Applications/freesurfer/subjects/fsaverage/surf/lh.thickness >> srcsubjid = fsaverage >> srcsurf= white >> srcframe = 0 >> thsign = abs >> thmin = 0 >> thmax = -1 >> fdr= -1 >> minarea= 0 >> xfmfile= talairach.xfm >> clabelfile = ./tests_label/sub/lh.amygdala.label >> clabelinv = 0 >> nth = -1 >> sumfile = ./tests_label/sum/sum.lh.amygdala >> subjectsdir= /Applications/freesurfer/subjects >> FixMNI = 0 >> Loading clabel ./tests_label/sub/lh.amygdala.label. >> Found 1941 points in clabel. >> - XFM matrix (RAS2RAS) --- >> /Applications/freesurfer/subjects/fsaverage/mri/transforms/talairach.xfm >> 1.0 0.0 0.0 0.0; >> 0.0 1.0 0.0 0.0; >> 0.0 0.0 1.0 0.0; >> 0.0 0.0 0.0 1.0; >> >> Reading source surface >> /Applications/freesurfer/subjects/fsaverage/surf/lh.white >> Done reading source surface >> Computing metric properties >> Loading source values >> /Applications/freesurfer/bin/mri_surfcluster: line 3: 2828 Bus error: 10 >>mri_surfcluster.bin "$@" >> >> Maybe because lh.thickness is only for cortical regions? In this case, how >> can I obtain centroids of subcortical ROIs? >> >> Thanks >> Regards >> Lucia >> >> >> >> >> Hi Lucia >> >> the first column being -1 means that it is not mapped to the surface, so is >> correct in your (subcortical) case. Try loading the label as an ROI in >> freeview and see if it is correct >> >> cheers >> Bruce >> >> >> Hi Lucia >> >> the first column being -1 means that it is not mapped to the surface, so is >> correct in your (subcortical) case. Try loading the label as an ROI in >> freeview and see if it is correct >> >> cheers >> Bruce >> >> Dear Brouce, >> >> >> thanks again. >> I would like exactly how to set mri_vol2label for subcortical regions as the >> way I used give me all the values of the first column equal to -1. This is a >> problem when I want to obtain obtain the centroid of the ROI using &g
