Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

grossly abormal brain
by Krieger, Donald N. 17 Nov '15

17 Nov '15

A few cuts from a grossly abnormal scan are attached. Do you think freesurfer can effectively segment this one? If so, please point us in the right direction to get started with it. Thanks. - Don

3 3

SNR Tracula
by Scott Quadrelli 17 Nov '15

17 Nov '15

Hi, Tracula outputs the SNR for each volume in a txt file. I was wondering if anyone can point me to some literature on how the SNR is being calculated? Cheers, Scott Quadrelli

2 2

Problem with hippocampal subfields segmentation FS v6
by Gronenschild Ed (NP) 17 Nov '15

17 Nov '15

Hi, At the very beginning of the hippocampal subfields segmentation the following message window popped up: segmentSubjectT1_autoEstimateAlveusML cannot be opened because of a problem. Check with the developer to make sure segmentSubjectT1_autoEstimateAlveusML works with this version of Mac OS X. .... etc. I have installed Matlab runtime and also Java Runtime Environment: Mac OSX10.7.5 the command "uname -m" outputs x86_64 FreeSurfer V6 beta release 15 Oct 2015 Cheers, Ed

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R: R: Re: R: Re: R: Re: R: Re: average z-score of each subject from a common cluster
by stdp82＠virgilio.it 17 Nov '15

17 Nov '15

I have run cat ... /my-glm.wls/group.diff/cache.th13.neg.sig.cluster.summary and I have obtained ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs Annot 1 -3.595 110577 865.93 11.8 39.4 -0.1 0.00620 0.00520 0.00720 1672 rostralanteriorcingulate after mri_segstats --seg .../my-glm.wls/group.diff/cache.th13.neg.sig. cluster.nii.gz --i Control21/rest/fc.seed.surf.rh/R_Seed/z.nii.gz -- sum summaryfile_Control and summary file is: # ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev Min Max Range 1 -2 1672 1672.0 Seg-002 -2.2757 2.2172 -6.4504 2.5762 9.0266 2 0 162170 162170.0 Seg0000 1.3956 1.6398 -7.0471 14.1452 21.1923 I have two raw. Which is the raw which contains the average z-score in the cluster? What's meaning, in term of location, Seg-002/0? In cluster. cache.th13.neg.sig.cluster.summary contains only rostralanteriorcingulate. Thanks, Stefano > > > >>>----Messaggio originale---- >>>Da: greve(a)nmr.mgh.harvard.edu >>>Data: 9-nov-2015 23.59 >>>A: <freesurfer(a)nmr.mgh.harvard.edu> >>>Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: average z-score of each >>subject from a common cluster >>> >>> >>> >>>On 11/07/2015 07:29 PM, stdp82(a)virgilio.it wrote: >>>> Thanks. But what's meaning "colheader"? >>>Column header. The title of the column >>>> In my cache.th13.neg.sig.masked.nii.gz I have only a significant >>ROI. >>>> In the summary file there are five column and 5 different value of >>>> "mean". >>>> Which is the correct, expressing the mean z-score of the cluster? >>>The column labeled "Mean", probably the 6th column >>>> >>>> Stefano >>>> >>>>> ----Messaggio originale---- >>>>> Da: greve(a)nmr.mgh.harvard.edu >>>>> Data: 6-nov-2015 23.07 >>>>> A: <freesurfer(a)nmr.mgh.harvard.edu> >>>>> Ogg: Re: [Freesurfer] R: Re: R: Re: average z-score of each >>subject >>>> from a common cluster >>>>> under the "Mean" column >>>>> >>>>> On 11/06/2015 07:46 AM, stdp82(a)virgilio.it wrote: >>>>>> I have run >>>>>> mri_segstats --seg .../my-glm.wls/group.diff/cache.th13.neg. sig. >>>> masked. >>>>>> nii.gz rh parc --i subj/fc.seed.surf.rh/R_seed/z.nii.gz --sum >>>>>> summaryfile >>>>>> >>>>>> and I have obtained 9 columns and 5 rows. >>>>>> I'm confused on results. Where is the mean z-score for cache. >>th13. >>>> neg. >>>>>> sig.masked.nii.gz? >>>>>> >>>>>> # ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean >>StdDev >>>>>> Min Max Range >>>>>> 1 -4 7 7.0 Seg-004 -2.4544 0.5023 >>>>>> -3.2164 -1.7619 1.4545 >>>>>> 2 -3 153 153.0 Seg-003 -2.6662 1.4724 >>>>>> -6.2120 1.7587 7.9707 >>>>>> 3 -2 848 848.0 Seg-002 -2.4930 2.0088 >>>>>> -6.4504 2.3528 8.8032 >>>>>> 4 -1 1518 1518.0 Seg-001 -2.1416 1.6727 >>>>>> -6.4227 2.5420 8.9648 >>>>>> 5 0 161316 161316.0 Seg0000 1.4152 1.6218 >>>>>> -7.0471 14.1452 21.1923 >>>>>> >>>>>> Because my data are on surface mri_surfcluster should be >helpful? >>>>>> >>>>>> Thanks. >>>>>> >>>>>> >>>>>> Stefano >>>>>> >>>>>> >>>>>>> ----Messaggio originale---- >>>>>>> Da: greve(a)nmr.mgh.harvard.edu >>>>>>> Data: 3-nov-2015 19.55 >>>>>>> A: <freesurfer(a)nmr.mgh.harvard.edu> >>>>>>> Ogg: Re: [Freesurfer] R: Re: average z-score of each subject >>from >>>> a >>>>>> common cluster >>>>>>> look in the summaryfile. Also, don't use --seg z.nii.gz. In the >>>>>> command >>>>>>> below, it works because you have --annot afterwards, but in >>>> general >>>>>> it >>>>>>> is not correct >>>>>>> >>>>>>> On 10/30/2015 04:22 PM, stdp82(a)virgilio.it wrote: >>>>>>>> Thanks. >>>>>>>> I have obtained: >>>>>>>> >>>>>>>> $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ >>>>>>>> >>>>>>>> cwd >>>>>>>> >>>>>>>> cmdline mri_segstats --seg z.nii.gz --annot Control21_FS rh >>aparc >>>> -- >>>>>> i >>>>>>>> z.nii.gz --sum summaryfile >>>>>>>> >>>>>>>> sysname Darwin >>>>>>>> >>>>>>>> hostname iMac-di-Stefano.local >>>>>>>> >>>>>>>> machine x86_64 >>>>>>>> >>>>>>>> user Stefano >>>>>>>> >>>>>>>> UseRobust 0 >>>>>>>> >>>>>>>> Loading z.nii.gz >>>>>>>> >>>>>>>> Loading z.nii.gz >>>>>>>> >>>>>>>> Voxel Volume is 1 mm^3 >>>>>>>> >>>>>>>> Generating list of segmentation ids >>>>>>>> >>>>>>>> Found 22 segmentations >>>>>>>> >>>>>>>> Computing statistics for each segmentation >>>>>>>> >>>>>>>> 0 -7 2 2.000 >>>>>>>> >>>>>>>> 1 -6 110 110.000 >>>>>>>> >>>>>>>> 2 -5 255 255.000 >>>>>>>> >>>>>>>> 3 -4 518 518.000 >>>>>>>> >>>>>>>> 4 -3 1190 1190.000 >>>>>>>> >>>>>>>> 5 -2 1692 1692.000 >>>>>>>> >>>>>>>> 6 -1 4104 4104.000 >>>>>>>> >>>>>>>> 7 0 61577 61577.000 >>>>>>>> >>>>>>>> 8 1 42598 42598.000 >>>>>>>> >>>>>>>> 9 2 28146 28146.000 >>>>>>>> >>>>>>>> 10 3 14859 14859.000 >>>>>>>> >>>>>>>> 11 4 5845 5845.000 >>>>>>>> >>>>>>>> 12 5 1899 1899.000 >>>>>>>> >>>>>>>> 13 6 485 485.000 >>>>>>>> >>>>>>>> 14 7 116 116.000 >>>>>>>> >>>>>>>> 15 8 75 75.000 >>>>>>>> >>>>>>>> 16 9 74 74.000 >>>>>>>> >>>>>>>> 17 10 78 78.000 >>>>>>>> >>>>>>>> 18 11 65 65.000 >>>>>>>> >>>>>>>> 19 12 104 104.000 >>>>>>>> >>>>>>>> 20 13 45 45.000 >>>>>>>> >>>>>>>> 21 14 5 5.000 >>>>>>>> >>>>>>>> >>>>>>>> How I can know the meaning of this number? Where is z? >>>>>>>> >>>>>>>> I have tried also with: >>>>>>>> >>>>>>>> mri_segstats --seg z.nii.gz --annot Control_21 rh aparc --i z. >>>> nii. >>>>>> gz >>>>>>>> --sum summaryfile --mask >>>>>>>> .../fc.ramgseed.surf.rh/R_Amygdala/my-glm.wls/group. >diff/cache. >>>> th13. >>>>>> neg.sig.masked.nii.gz >>>>>>>> --avgwfvol mrivol >>>>>>>> >>>>>>>> >>>>>>>> but I have problem with interpretation. >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> Stefano >>>>>>>> >>>>>>>> >>>>>>>> ----Messaggio originale---- >>>>>>>> Da: greve(a)nmr.mgh.harvard.edu >>>>>>>> Data: 30-ott-2015 16.17 >>>>>>>> A: <freesurfer(a)nmr.mgh.harvard.edu> >>>>>>>> Ogg: Re: [Freesurfer] average z-score of each subject >>from a >>>>>>>> common cluster >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> On 10/30/15 7:16 AM, stdp82(a)virgilio.it wrote: >>>>>>>>> Hi list, >>>>>>>>> I have two queries, please. >>>>>>>>> >>>>>>>>> I'd like to have the z-score from my rsfMRI data (seed- >>>>>> analyis). >>>>>>>>> 1) I have extract the z-score from the Vtx Max >>>>>>>>> >>>>>>>>> In details, after groups comparison analysis, I have >>opened >>>>>>>>> the cache.th13.pos.sig.cluster.summary contained in >>group. >>>> diff >>>>>>>>> folder and I have read the Vtx Max coordinates. >>>>>>>>> Next, I have open the z.nii.gz of each subject and I >>have >>>>>>>>> expected the z-score from the vertex which have the >Vtx >>Max >>>>>>>>> coordinates. >>>>>>>>> >>>>>>>>> Is this procedure corrected? >>>>>>>> Yes >>>>>>>>> 2) z-score of each subject from a common cluster >>>>>>>>> >>>>>>>>> I would like to use the cluster which shows the group >>>>>> difference >>>>>>>>> (cache.th13.pos.sig.cluster.nii.gz) as ROI mask. Thus, >I >>>> would >>>>>>>>> extract from it the average of the z-score which is >>>> contained >>>>>> in >>>>>>>>> each subject. >>>>>>>>> How should I do? >>>>>>>> Use mri_segstats passing the z map as the input (--i) >and >>>> the >>>>>>>> cluster map as the seg. The output will be --sum. Run >>with >>>> -- >>>>>> help >>>>>>>> for more info >>>>>>>>> Thanks. >>>>>>>>> >>>>>>>>> >>>>>>>>> Stefano >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> Freesurfer mailing list >>>>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>>>> https://mail.nmr.mgh.harvard. >>>> edu/mailman/listinfo/freesurfer >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Freesurfer mailing list >>>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>> -- >>>>>>> Douglas N. Greve, Ph.D. >>>>>>> MGH-NMR Center >>>>>>> greve(a)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(a)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(a)nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>>> >>>>> -- >>>>> Douglas N. Greve, Ph.D. >>>>> MGH-NMR Center >>>>> greve(a)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(a)nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>> >>>-- >>>Douglas N. Greve, Ph.D. >>>MGH-NMR Center >>>greve(a)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(a)nmr.mgh.harvard.edu >>>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >> >>_______________________________________________ >>Freesurfer mailing list >>Freesurfer(a)nmr.mgh.harvard.edu >>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >

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R: R: Re: R: Re: R: Re: R: Re: error MRS voxel as seed in FS-FAST
by stdp82＠virgilio.it 17 Nov '15

17 Nov '15

Thanks. But the MRS_mask should be in Tal, MNI or native? Now I'm using a masks that overlaps orig.nii.gz. Second, if I would like to create a sphere and use it as seed, there is a specific command line? Stefano >>----Messaggio originale---- >>Da: greve(a)nmr.mgh.harvard.edu >>Data: 9-nov-2015 23.24 >>A: <freesurfer(a)nmr.mgh.harvard.edu> >>Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: error MRS voxel as seed in >FS-FAST >> >>So that mask has 22926 non-zero voxels? The only other thing I can >think >>of is that the registration is off. Have you checked that? >> >>On 11/06/2015 07:16 AM, stdp82(a)virgilio.it wrote: >>> I hope that this information are fine >>> >>> fslinfo $SUBJECTS_DIR/Control22/MRS_MASK.nii.gz >>> data_type FLOAT32 >>> dim1 256 >>> dim2 256 >>> dim3 256 >>> dim4 1 >>> datatype 16 >>> pixdim1 1.000000 >>> pixdim2 1.000000 >>> pixdim3 1.000000 >>> pixdim4 0.000000 >>> cal_max 0.0000 >>> cal_min 0.0000 >>> file_type NIFTI-1+ >>> >>> >>> fslstats $SUBJECTS_DIR/Control22/MRS_MASK.nii.gz -V >>> 22926 22926.000000 >>> >>> Thanks, >>> >>> >>> Stefano >>> >>> >>>> ----Messaggio originale---- >>>> Da: greve(a)nmr.mgh.harvard.edu >>>> Data: 5-nov-2015 23.43 >>>> A: <freesurfer(a)nmr.mgh.harvard.edu> >>>> Ogg: Re: [Freesurfer] R: Re: R: Re: error MRS voxel as seed in FS- >>> FAST >>>> How many non-zero voxels are in MRS_MASK.mgz? Is MRS_MASK.mgz >256^3, >>> 1mm3 ? >>>> On 11/05/2015 04:47 PM, stdp82(a)virgilio.it wrote: >>>>> Please see the file attached. >>>>> Thanks >>>>> >>>>> Stefanofile >>>>> >>>>> ----Messaggio originale---- >>>>> Da: greve(a)nmr.mgh.harvard.edu >>>>> Data: 5-nov-2015 15.43 >>>>> A: <freesurfer(a)nmr.mgh.harvard.edu> >>>>> Ogg: Re: [Freesurfer] R: Re: error MRS voxel as seed in FS- >FAST >>>>> >>>>> sorry, should have been >>>>> >>>>> fcseed-sess -debug -s Control22_FS -cfg MRS_MASK.config |& >tee >>> doug.log >>>>> >>>>> >>>>> On 11/4/15 6:05 PM, stdp82(a)virgilio.it wrote: >>>>>> Hi Dough, >>>>>> in summary: >>>>>> I have the MRS_MASK.mgz within $SUBJECTS_DIR/Control22/mri >>>>>> thus, I have copy this file in fMRI directory >>> (fMRI/Control22_FS) the >>>>>> MRS_MASK.mgz >>>>>> and run: >>>>>> fcseed-config -segid 1 -seg Control22_FS/MRS_MASK.mgz -fsd >>> rest -mean - >>>>>> cfg MRS_MASK.config >>>>>> fcseed-sess -s Control22_FS -cfg MRS_MASK.config >>>>>> >>>>>> ...Writing to >>>>>> >>> /Applications/freesurfer/subjects/fMRI/Control22_FS/rest/001/tmp. >>> fcseed- >>>>>> sess.12305/avgwf.mgh >>>>>> Segmentation fault >>>>>> >>>>>> Therefore, according with your suggestion, I have now run: >>>>>> fcseed-sess -debug -s -cfg MRS_MASK.config | & tee doug. log >>>>>> ERROR: cound not find session -cfg >>>>>> >>>>>> The doug.log is attached. >>>>>> >>>>>> Thanks, >>>>>> >>>>>> >>>>>> Stefano >>>>>> >>>>>> >>>>>> >>>>>> >>>>>>> ----Messaggio originale---- >>>>>>> Da:greve@nmr.mgh.harvard.edu >>>>>>> Data: 4-nov-2015 16.58 >>>>>>> A:<freesurfer(a)nmr.mgh.harvard.edu> >>>>>>> Ogg: Re: [Freesurfer] error MRS voxel as seed in FS-FAST >>>>>>> >>>>>>> First, when running fcseed-config, don't give it the full >>> path, just >>>>>> the >>>>>>> path relative to subject/mri (in this case only MRS_MASK. >mgz) >>>>>>> >>>>>>> However, I don't think that is the problem. Please run >>>>>>> >>>>>>> fcseed-sess -debug -s -cfg MRS_MASK.config |& tee doug. log >>>>>>> >>>>>>> and send me doug.log >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> On 11/04/2015 04:14 AM,stdp82(a)virgilio.it wrote: >>>>>>>> Hi list, this error is still occurring: >>>>>>>> >>>>>>>> mri_convert $SUBJECTS_DIR/subj/mri/MRS_MASK.nii.gz >>>>>>>> $SUBJECTS_DIR//subj/mri/MRS_MASK.mgz >>>>>>>> fcseed-config -segid 1 -seg >$SUBJECTS_DIR//subj/mri/MRS_MASK. >>> mgz - >>>>>> fsd >>>>>>>> rest -mean -cfg MRS_MASK.config >>>>>>>> fcseed-sess -s -cfg MRS_MASK.config >>>>>>>> >>>>>>>> During >>>>>>>> >>>>>>>> fcseed-sess -s subj -cfg MRS_MASK.config >>>>>>>> >>>>>>>> Voxel Volume is 64.5752 mm^3 >>>>>>>> Generating list of segmentation ids >>>>>>>> Found 1 segmentations >>>>>>>> Computing statistics for each segmentation >>>>>>>> 0 1 0 >>> 0.000 >>>>>>>> MRIalloc(0, 1, 1): bad parm >>>>>>>> Reporting on 0 segmentations >>>>>>>> Computing spatial average of each frame >>>>>>>> >>>>>>>> Writing to >>> /Applications/freesurfer/subjects/fMRI/sub/rest/001/tmp. >>>>>>>> fcseed-sess.97908/avgwf.mgh >>>>>>>> Segmentation fault >>>>>>>> >>>>>>>> I have read your previous message and you can check the >MRS >>> voxel >>>>>>>> features. >>>>>>>> MRS voxel mask is in subj directory where I have run >recon >>> all - >>>>>> all. >>>>>>>> data_type FLOAT32 >>>>>>>> dim1 256 >>>>>>>> dim2 256 >>>>>>>> dim3 256 >>>>>>>> dim4 1 >>>>>>>> datatype 16 >>>>>>>> pixdim1 1.000000 >>>>>>>> pixdim2 1.000000 >>>>>>>> pixdim3 1.000000 >>>>>>>> pixdim4 0.010747 >>>>>>>> cal_max 0.0000 >>>>>>>> cal_min 0.0000 >>>>>>>> file_type NIFTI-1+ >>>>>>>> >>>>>>>> >>>>>>>> The features are same of other subject that runs fine. >>>>>>>> data_type FLOAT32 >>>>>>>> dim1 256 >>>>>>>> dim2 256 >>>>>>>> dim3 256 >>>>>>>> dim4 1 >>>>>>>> datatype 16 >>>>>>>> pixdim1 1.000000 >>>>>>>> pixdim2 1.000000 >>>>>>>> pixdim3 1.000000 >>>>>>>> pixdim4 0.010747 >>>>>>>> cal_max 0.0000 >>>>>>>> cal_min 0.0000 >>>>>>>> file_type NIFTI-1+ >>>>>>>> >>>>>>>> Thank you very much. >>>>>>>> >>>>>>>> >>>>>>>> Stefano >>>>>>>> >>>>>>>> >>>>>>>>> ----Messaggio originale---- >>>>>>>>> Da:stdp82@virgilio.it >>>>>>>>> Data: 16-ott-2015 23.15 >>>>>>>>> A:<freesurfer(a)nmr.mgh.harvard.edu> >>>>>>>>> Ogg: [Freesurfer] R: Re: R: import FS-FAST results in >FSL >>>>>>>>> >>>>>>>>> I'd like to open with FSLview the sig.nii.gz which is >>> produced by >>>>>>>>> selxavg3-sess. >>>>>>>>> If I use mri_surf2vol, which is the template to added in >-- >>>>>> template? >>>>>>>>> It should be in Tailairach space? Where can I find the >>> template >>>>>> that >>>>>>>> I >>>>>>>>> should added? >>>>>>>>> Thanks, >>>>>>>>> >>>>>>>>> Stefano >>>>>>>>> >>>>>>>>> subj/rest/fc.seed.surf.lh/L_seed/sig.nii.gz >>>>>>>>> data_type FLOAT32 >>>>>>>>> dim1 27307 >>>>>>>>> dim2 1 >>>>>>>>> dim3 6 >>>>>>>>> dim4 1 >>>>>>>>> datatype 16 >>>>>>>>> pixdim1 1.000000 >>>>>>>>> pixdim2 1.000000 >>>>>>>>> pixdim3 1.000000 >>>>>>>>> pixdim4 1100.000000 >>>>>>>>> cal_max 49.1815 >>>>>>>>> cal_min -12.3855 >>>>>>>>> file_type NIFTI-1+ >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> Thanks, >>>>>>>>> >>>>>>>>> Stefano >>>>>>>>> >>>>>>>>> >>>>>>>>>> ----Messaggio originale---- >>>>>>>>>> Da:greve@nmr.mgh.harvard.edu >>>>>>>>>> Data: 29-set-2015 22.09 >>>>>>>>>> A:<freesurfer(a)nmr.mgh.harvard.edu> >>>>>>>>>> Ogg: Re: [Freesurfer] R: import FS-FAST results in FSL >>>>>>>>>> >>>>>>>>>> Do you mean surface-based analysis? You'd have to put >them >>> back >>>>>>>> into >>>>>>>>> the >>>>>>>>>> volume using mri_surf2vol, write them out as nifti and >>> then run >>>>>>>>> fslview >>>>>>>>>> on them >>>>>>>>>> >>>>>>>>>> On 09/29/2015 11:17 AM,stdp82(a)virgilio.it wrote: >>>>>>>>>>> Hi list, >>>>>>>>>>> >>>>>>>>>>> I would like to import FS-FAST results >(conjunction >>> maps) >>>>>> in >>>>>>>>> FSL, >>>>>>>>>>> opening them by fslview. >>>>>>>>>>> Could you provide me any suggestion? >>>>>>>>>>> >>>>>>>>>>> Thank you very much >>>>>>>>>>> Best regards, >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> Stefano >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> _______________________________________________ >>>>>>>>>>> Freesurfer mailing list >>>>>>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>>>>>> https://mail.nmr.mgh.harvard. >>> edu/mailman/listinfo/freesurfer >>>>>>>>>> -- >>>>>>>>>> Douglas N. Greve, Ph.D. >>>>>>>>>> MGH-NMR Center >>>>>>>>>> greve(a)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(a)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(a)nmr.mgh.harvard.edu >>>>>>>>> https://mail.nmr.mgh.harvard. >>> edu/mailman/listinfo/freesurfer >>>>>>>> _______________________________________________ >>>>>>>> Freesurfer mailing list >>>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>>> https://mail.nmr.mgh.harvard. >edu/mailman/listinfo/freesurfer >>>>>>>> >>>>>>>> >>>>>>> -- >>>>>>> Douglas N. Greve, Ph.D. >>>>>>> MGH-NMR Center >>>>>>> greve(a)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(a)nmr.mgh.harvard.edu >>>>>>> https://mail.nmr.mgh.harvard. >edu/mailman/listinfo/freesurfer >>>>>>> >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Freesurfer mailing list >>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>> https://mail.nmr.mgh.harvard. >edu/mailman/listinfo/freesurfer >>>>> >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> -- >>>> Douglas N. Greve, Ph.D. >>>> MGH-NMR Center >>>> greve(a)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(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >> >>-- >>Douglas N. Greve, Ph.D. >>MGH-NMR Center >>greve(a)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(a)nmr.mgh.harvard.edu >>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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selxavg3-sess error
by Danielle Miller 16 Nov '15

16 Nov '15

Hello Freesurfer Experts, I keep running into the following error (see below) when selxavg3-sess gets to my third subject. I am assuming this is because this subject does not have all of the conditions modeled (that is, this particular subject does not have any incorrect responses). Is there a way to model an empty condition to get around this? I want a general contrast of Incorrect > Correct, but some subjects do not make any errors and therefore would not have this condition in their paradigm files. Any advice would be greatly appreciated. #@# CC_003_recon ############################### /Volumes/VA_Imaging/Projects/dmiller/COGCON/FSFAST/CC_003_recon ------------------------- $Id: fast_selxavg3.m,v 1.100 2011/03/02 16:14:38 greve Exp $ /Applications/freesurfer/fsfast/toolbox/fast_selxavg3.m /Applications/freesurfer/fsfast/toolbox/fast_ldanaflac.m /Applications/freesurfer-5.3/matlab/MRIread.m ------------------------- outtop = /Volumes/VA_Imaging/Projects/dmiller/COGCON/FSFAST Extension format = nii.gz INFO: key PerSession unrecognized, line 6, skipping INFO: key ApplySubCortMask unrecognized, line 12, skipping 1 Correct-v-Incorrect.mat 2 Incorrect-v-base.mat nruns = 4 autostimdur = outanadir = /Volumes/VA_Imaging/Projects/dmiller/COGCON/FSFAST/CC_003_recon/Bold1/correct.sm15.mni305 Found 57600/537168 (10.7) voxels in mask Creating Design Matrix ... creation time = 0.008 sec DoMCFit = 1 ntptot = 740, nX = 27, DOF = 713 Saving X matrix to /Volumes/VA_Imaging/Projects/dmiller/COGCON/FSFAST/CC_003_recon/Bold1/correct.sm15.mni305/Xtmp.mat ??? Error using ==> svd Input to SVD must not contain NaN or Inf. Error in ==> cond at 39 s = svd(A); Error in ==> fast_selxavg3 at 254 XCond = cond(XtX); >> ------------------------------------------ ERROR: fast_selxavg3() failed\n Thanks, Danielle -- Ph.D. Program in Behavioral Neuroscience Boston University School of Medicine L-815 72 E. Concord St Boston, MA 02118 VA Boston Healthcare System Jamaica Plain Memory Disorders Research Center 150 South Huntington Ave D11-103 Boston, MA 02130 OFFICE:(857) 364-2130

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aparcstats2table -- extracting multiple measures
by Eryilmaz, H. Hamdi 16 Nov '15

16 Nov '15

Dear experts, I am using aparcstats2table to extract values on a number of measures like thickness, curvature, folding index, and surface area for specific ROIs. Is it possible to create a table (using aparcstats2table) with all these measures included or do I have to run it separately and create a separate table for each measure? Passing --meas flag multiple items did not work. Thanks for your help! Hamdi

3 6

Issue with Talairach - mritotal
by Amlung, Michael 16 Nov '15

16 Nov '15

1 0

Re: [Freesurfer] Advice for FreeSurfer developers
by Gronenschild Ed (NP) 16 Nov '15

16 Nov '15

Hi Doug, I used mostly the default options, nothing special: recon-all -autorecon1 -clean-tal -expert my_options.txt -hires where the file my_options.txt contains some options for nu_correct. Then I entered recon-all -autorecon2 -autorecon3 -hippocampal-subfields-T1 -hires The error occurred with the last recon-all command. BTW, I really don't know if the -clean-tal option is needed with FS v6. Cheers Ed On 11 Nov 2015, at 18:00, <freesurfer-request(a)nmr.mgh.harvard.edu<mailto:freesurfer-request@nmr.mgh.harvard.edu>> wrote: Message: 9 Date: Wed, 11 Nov 2015 11:08:46 -0500 From: Douglas Greve <greve(a)nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] Advice for FreeSurfer developers To: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Message-ID: <5643680E.1030800(a)nmr.mgh.harvard.edu<mailto:5643680E.1030800@nmr.mgh.harvard.edu>> Content-Type: text/plain; charset=windows-1252; format=flowed Hi Ed, generally recon-all does not need matlab. Are you running the gyrification analysis? That should be the only thing that needs matlab. doug On 11/11/15 6:14 AM, Gronenschild Ed (NP) wrote: Dear developers, Is it possible to check the presence of Matlab runtime right at the start of recon-all in FreeSurfer v6 instead of a long way down in the pipeline. After 36 hours for a high-res data processing I got this unexpected error message. Thanks in advance. Cheers Ed _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

2 1

very large csf spaces
by Krieger, Donald N. 16 Nov '15

16 Nov '15

This is a newbie question as this is the first grossly abnormal scan on which I need to run freesurfer. There are very large CSF spaces and only a rim of cortex and white matter for many regions. Freesurfer fails very early on. Before I post errors, I would like to try to get it to complete if there are pointers online. Is there a tutorial for running freesurfer on a grossly abnormal scan? Are there standard rules of thumb? Thanks - Don

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