Freesurfer May 2014

freesurfer@nmr.mgh.harvard.edu

139 participants
206 discussions

Re: [Freesurfer] kvlQuantify naming problem [possible fix]
by C.P. Frost 21 May '14

21 May '14

Follow-up: I then run into indexing problems when calling freeview with subfield volumes (similar to http://bit.ly/1pdEWRZ) which leads me to believe kvlQuantify is the only script that relies on the old convention. Changing the names back to CA2_3.mgz, etc., fixes THAT problem. Rather than changing the filenames to the old convention, it's probably better to fix the script and leave the filenames alone. On Wed, May 21, 2014 at 1:06 PM, C.P. Frost <carfro(a)gmail.com> wrote: > Hello all, > > My site has recently upgraded to the newest version of Freesurfer, and > I've run a set of subjects on recon-all using the hippocampal subfield > segmentation flag. Everything went well. Then in running > kvlQuantifyHippocampalSubfieldSegmentations.sh, I received error messages > indicating that certain expected files didn't exist. > > In particular, among output files labeled with the scheme > $subj/mri/posterior_$side_$struct.mgz, the script expected ...CA2-3.mgz and > ...CA4-DG.mgz, and existing files were named ...CA2_3.mgz and ...CA4_DG.mgz > -- in other words, the script expected a hyphen but instead the filenames > contained an underscroe. > > After renaming the files appropriately, kvlQuantify... successfully > generated the nonPartialVolumeStats files and everything worked fine. > > I didn't see any threads with this solution, and only one or two that > mentioned the problem (http://bit.ly/1vHbV5K) so I thought I'd offer it > up in case it could be addressed in a future release. > > Cheers, > C.P. Frost >

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Compatibility Tracula v.5.3 and recon v.5.2 longitudinal
by Chung, Yoonho 21 May '14

21 May '14

Hi Anastasia, I have a large set of freesurfer recons (T1) already processed through FS version 5.2 longitudinal stream while ago. However, I see now that there is an advantage of using Tracula 5.3 longitudinal stream for DTI longitudinal analysis. Do you know if I run the DWI data using 5.3 TRACULA longitudinal stream - if it will work with recons that are processed with 5.2? Thanks! Y

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surface-based morphometry registration
by Tudor Popescu 21 May '14

21 May '14

Hi all, If I understand correctly, the surface-based morphometry (SBM) done by Freesurfer offers superior registration as compared to voxel-based methods such as VBM, in that: 1. "SBM smoothing respects anatomical boundaries better than the 3D VBM smoothing". 2. "SBM group analysis employs inter-subject alignment based on the patterns of sulci and gyri, as opposed to Talairach registration, which often ignores sulcal/gyral landmarks" I'm not sure I understand those reasons, however. For 1., why does the smoothing operation (basically, a multiplication) "care" about anatomy or registration at all, such that it can be said it is better done in SBM vs VBM? And for 2., doesn't the Talairach registration used in VBM simply imply a certain target template? Surely such a template is used in SBM registration as well, and if that is the case, then how are sulcal/gyral landmarks taken into account? Thanks for any help! Tudor

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mri_convert frame error in tracula
by Pedro Rosa 21 May '14

21 May '14

Dear All, As suggested, I am reposting a previous question. I am trying to run a single subject in TRACULA (trac-all -corr -c config), 148, for who there is a folder ‘1482’ with all DWI DICOMs and a folder ‘ESNA148’ with the recon-all processing (Freesurfer 5.3). Also in $SUBJECTS_DIR there is bval.bval and bvec.bvec. I attached the trac-all.log that comes with the following error: ERROR: fMRIframe: frame >= frames Can anyone help me? Thank you in advance! Regards, Pedro Rosa.

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recon-all mri_nu_correct error
by Durai Arasan 21 May '14

21 May '14

Hi Freesurfer experts, I was running recon-all on a cluster and encountered the following error: mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz Linux compute-g20-12.deepthought.umd.edu 2.6.18-371.3.1.el5 #1 SMP Mon Nov 11 03:23:58 EST 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s hcp80100307 exited with ERRORS at Wed May 21 12:43:36 EDT 2014 Any idea whats the source of the error? Thanks! On Wed, May 21, 2014 at 2:20 PM, C.P. Frost <cpfrost(a)wisc.edu> wrote: > Hello all, > > My site has recently upgraded to the newest version of Freesurfer, and > I've run a set of subjects on recon-all using the hippocampal subfield > segmentation flag. Everything went well. Then in running > kvlQuantifyHippocampalSubfieldSegmentations.sh, I received error messages > indicating that certain expected files didn't exist. > > In particular, among output files labeled with the scheme > $subj/mri/posterior_$side_$struct.mgz, the script expected ...CA2-3.mgz and > ...CA4-DG.mgz, and existing files were named ...CA2_3.mgz and ...CA4_DG.mgz > -- in other words, the script expected a hyphen but instead the filenames > contained an underscroe. > > After renaming the files appropriately, kvlQuantify... successfully > generated the nonPartialVolumeStats files and everything worked fine. > > I didn't see any threads with this solution, and only one or two that > mentioned the problem (http://bit.ly/1vHbV5K) so I thought I'd offer it > up in case it could be addressed in a future release. > > Cheers, > C.P. Frost > > _______________________________________________ > 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. > >

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kvlQuantify naming problem [possible fix]
by C.P. Frost 21 May '14

21 May '14

Hello all, My site has recently upgraded to the newest version of Freesurfer, and I've run a set of subjects on recon-all using the hippocampal subfield segmentation flag. Everything went well. Then in running kvlQuantifyHippocampalSubfieldSegmentations.sh, I received error messages indicating that certain expected files didn't exist. In particular, among output files labeled with the scheme $subj/mri/posterior_$side_$struct.mgz, the script expected ...CA2-3.mgz and ...CA4-DG.mgz, and existing files were named ...CA2_3.mgz and ...CA4_DG.mgz -- in other words, the script expected a hyphen but instead the filenames contained an underscroe. After renaming the files appropriately, kvlQuantify... successfully generated the nonPartialVolumeStats files and everything worked fine. I didn't see any threads with this solution, and only one or two that mentioned the problem (http://bit.ly/1vHbV5K) so I thought I'd offer it up in case it could be addressed in a future release. Cheers, C.P. Frost

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Desikan Killiany Atlas measurements
by Buse Merve Ürgen 21 May '14

21 May '14

Dear all, I want to get the measurements of meancurvature, thickness, white matter volume and gray matter volume based on Desikan-Killiay Atlas. I would like to learn whether the commands I used to get them are the correct ones (in terms of content) & for Desikan Killiany atlas? *For meancurv: * aparcstats2table --hemi lh --subjects S1 S2 S3 --parc aparc --meas meancurv -t lh.parc.meancurv.txt *For thickness:* aparcstats2table --hemi rh --subjects S1 S2 S3 --parc aparc --meas meancurv -t rh.parc.meancurv.txt *For WM volume:* asegstats2table --all-segs --subjects S1 S2 S3 \-t table.wmparc.txt -d space --stats wmparc.stats *For GM volume:* aparcstats2table --subjects S1 S2 S3 --hemi lh --meas volume --parc=aparc --tablefile aparc_lh_volume_table.txt Thanks in advance,

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CTABreadASCII error with mris_label2annot
by Paul Beach 21 May '14

21 May '14

Freesurfer folks, I'm trying to compile an annotation using mris_label2annot after transferring fsaverage5 labels to a single subject. I'm getting a strange error. Essentially it looks like it can't find most of my transferred labels, which doesn't make sense as they are definitely in the directory in which I'm executing the command. The same error happens with both hemispheres. I am including an 'unknown' entry in the ctab files. I've tried changing things around with my ctab files and it looks like it just won't take in anything past the first '-l' flag in the mris_label2annot command. *Reading ctab rh.Yeo_7Net_split.ctab* *Number of ctab entries 2* *$Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $* *cwd /extern/research/PI/training/beachpau/Beach_FreeSurfer_data/HS_001/label* *cmdline mris_label2annot --s HS_001 --h rh --ctab rh.Yeo_7Net_split.ctab --annot Yeo_7Net_split_aparc --l rh.Background+FreeSurfer_Defined_Medial_Wall.label --l rh.7Networks_RH_Vis.label --l rh.7Networks_RH_SomMot.label --l rh.7Networks_RH_DorsAttn_Post.label --l rh.7Networks_RH_DorsAttn_FEF.label --l rh.7Networks_RH_DorsAttn_PrCv.label --l rh.7Networks_RH_SalVentAttn_TempOccPar.label --l rh.7Networks_RH_SalVentAttn_PrC.label --l rh.7Networks_RH_SalVentAttn_FrOper.label --l rh.7Networks_RH_SalVentAttn_PFCv.label --l rh.7Networks_RH_SalVentAttn_PFCl.label --l rh.7Networks_RH_SalVentAttn_Med.label --l rh.7Networks_RH_Limbic_OFC.label --l rh.7Networks_RH_Limbic_TempPole.label --l rh.7Networks_RH_Cont_Par.label --l rh.7Networks_RH_Cont_Temp.label --l rh.7Networks_RH_Cont_PFCv.label --l rh.7Networks_RH_Cont_PFCl.label --l rh.7Networks_RH_Cont_pCun.label --l rh.7Networks_RH_Cont_Cing.label --l rh.7Networks_RH_Cont_PFCmp.label --l rh.7Networks_RH_Default_Par.label --l rh.7Networks_RH_Default_Temp.label --l rh.7Networks_RH_Default_PFCv.label --l rh.7Networks_RH_Default_PFCm.label --l rh.7Networks_RH_Default_PCC.label * *sysname Linux* *hostname gauss.rad.msu.edu <http://gauss.rad.msu.edu>* *machine x86_64* *user beachpau* *subject HS_001* *hemi rh* *SUBJECTS_DIR /extern/research/PI/training/beachpau/Beach_FreeSurfer_data* *ColorTable rh.Yeo_7Net_split.ctab* *AnnotName Yeo_7Net_split_aparc* *nlables 26* *LabelThresh 0 0.000000* *Loading /extern/research/PI/training/beachpau/Beach_FreeSurfer_data/HS_001/surf/rh.orig* * 1 65793 rh.Background+FreeSurfer_Defined_Medial_Wall* * 2 -1 NOT_FOUND* * 3 -1 NOT_FOUND* * 4 -1 NOT_FOUND* * 5 -1 NOT_FOUND* * 6 -1 NOT_FOUND* * 7 -1 NOT_FOUND* * 8 -1 NOT_FOUND* * 9 -1 NOT_FOUND* *10 -1 NOT_FOUND* *11 -1 NOT_FOUND* *12 -1 NOT_FOUND* *13 -1 NOT_FOUND* *14 -1 NOT_FOUND* *15 -1 NOT_FOUND* *16 -1 NOT_FOUND* *17 -1 NOT_FOUND* *18 -1 NOT_FOUND* *19 -1 NOT_FOUND* *20 -1 NOT_FOUND* *21 -1 NOT_FOUND* *22 -1 NOT_FOUND* *23 -1 NOT_FOUND* *24 -1 NOT_FOUND* *25 -1 NOT_FOUND* *26 -1 NOT_FOUND* *Mapping unhit to unknown* *Found 5 unhit vertices* *Writing annot to /extern/research/PI/training/beachpau/Beach_FreeSurfer_data/HS_001/label/rh.Yeo_7Net_split_aparc.annot* I have attached my .ctab files in case they would help. -- Paul Beach DO/PhD candidate - Year VI Michigan State University - College of Osteopathic Medicine - Neuroscience Program - MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*)

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Re: [Freesurfer] R: Filipping issue
by Douglas N Greve 21 May '14

21 May '14

Hi Paola, please remember to post to the list and not to us personally. thanks! I would still use the xhemi tools for this. If you have N subjects, you will get 2*N surfaces aligned to the fsaverage_sym atlas. You can then just pick the ones you want to analyze further doug On 04/22/2014 08:34 AM, Paola Valsasina wrote: > Dear Doug, > > We have followed your suggestion and we performed the recon-all analysis for > all study subjects (till autorecon3) on non-flipped images. > > I am now reading the instructions on the wiki about the xhemi tool, but I am > not 100% sure they apply to our case. > > The wiki instructions describe a comparison between LH and RH within > subjects (i.e., an analysis of cortical asymmetry), whereas we would like > simply to L-R flip the final surfaces of patients having a RH damage, so > that all patients have the damage in the LH. > Then, we would like to compare them with control subjects. > > For this purpose, is it sufficient to register the patients lesioned in the > RH to the symmetric template with the --xhemi option? > > (i.e. surfreg --s subject_name --t fsaverage_sym --xhemi --rh --lh) > > Then, how do we perform final statistical analysis? > > Thank you in advance for any suggestion! > Kind regards > Paola > > > > Paola Valsasina, MSc > Research Fellow > Neuroimaging Research Unit (Director Prof. M. Filippi) > Institute of Experimental Neurology, Division of Neuroscience, > Scientific Institute and University "Vita-Salute" San Raffaele > Via Olgettina 60, 20132 Milan, Italy > > -------------------------------------------------------------------------- > IL MIO 5XMILLE VA AL SAN RAFFAELE DI MILANO > PERCHE' QUI LA RICERCA DIVENTA CURA. > CF 07636600962 > SE NON QUI, DOVE? > Info: 5xmille(a)hsr.it - http://www.5xmille.org/ > > > Disclaimer added by CodeTwo Exchange Rules 2007 > http://www.codetwo.com > > -----Messaggio originale----- > Da: freesurfer-bounces(a)nmr.mgh.harvard.edu > [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Per conto di Douglas N Greve > Inviato: giovedì 13 febbraio 2014 21.50 > A: freesurfer(a)nmr.mgh.harvard.edu > Oggetto: Re: [Freesurfer] Filipping issue > > > Definitely #2. You should use the xhemi tools > http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi > First run them through recon-all as normal, then follow the steps on the > wiki. Contact the list again to get instructions for the final analysis. > > doug > > > On 02/13/2014 08:23 AM, Paola Valsasina wrote: >> Dear List, >> >> we are starting the analysis of cortical thickness for a group of >> patients who have only one side affected. The majority of patients >> have the left hemisphere affected, but some patients have the right >> hemisphere affected. In order to do a group analysis, we would like to >> flip the images of some patients, so that the affected side is left >> for all subjects. >> >> Which is the best way to do this: >> >> 1)flip the 001.mgz volume and perform the entire recon-all pipeline >> with flipped images; >> >> or >> >> 2)perform the recon-all pipeline with the non-flipped volumes and flip >> only the final surfaces for statistical purposes? >> >> Thank you for any suggestion >> >> Kind regards >> >> Paola >> >> >> >> _______________________________________________ >> 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/

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change background color in tksurfer
by charujing123 21 May '14

21 May '14

Hi FS experts and users I want to change the background color of tksurfer from black to white. However I cannot find the drop-down list. Is there anyone who can tell me to desolve this? Thanks. All the best. Rujing Zha 2014-05-14 charujing123

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Freesurfer May 2014