Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

Viewing more than one label at once in Freeview?
by Gold, Andrea (NIH/NIMH) [F] 15 Dec '15

15 Dec '15

Hi, I am trying to show 3 aparc labels on the inflated surface, each in a different color, let’s say lh.inferiortemporal, lh.middletemporal and lh.superiortemporal . I have 2 questions: First I ran mris_annotation2label to extract the individual region aparc labels. I can merge them into a single label with mri_mergelabels, but when I do this both regions are in the same color. I alternatively tried mris_label2annot, as follows: mris_label2annot --s fsaverage --h lh --ctab /data/EDAN/freesurfer/buckner_data/tutorial_subjs/fsaverage/label/aparc.annot.ctab --a LeftTemporal_test --l labels/lh.middletemporal.label --l labels/lh.inferiortemporal.label --l labels/lh.superiortemporal.label Question 1) Should I be concerned that it says “bankssts, caudalanteriorcingulate, and caudalmiddlefrontla” in the output (copied below) and the freeview windw (see attached) even though I see ITG/MTG/STG on the brain in free view? Question 2) But, when I show the annotation file on the inflated brain in freeview, I can see the three region in 3 different colors, but the rest of the brain is a dark purple and hard to see. See attached image. Is there a way to change this so it looks like the inflated brain typically does? Or, is it possible to view more than one individual label at once? Thanks, Andrea [goldal2@biowulf label]$ mris_label2annot --s fsaverage --h lh --ctab /data/EDAN/freesurfer/buckner_data/tutorial_subjs/fsaverage/label/aparc.annot.ctab --a LeftTemporal_test --l labels/lh.middletemporal.label --l labels/lh.inferiortemporal.label --l labels/lh.superiortemporal.label Reading ctab /data/EDAN/freesurfer/buckner_data/tutorial_subjs/fsaverage/label/aparc.annot.ctab Number of ctab entries 36 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /gpfs/gsfs3/users/EDAN/freesurfer/buckner_data/tutorial_subjs/fsaverage/label cmdline mris_label2annot --s fsaverage --h lh --ctab /data/EDAN/freesurfer/buckner_data/tutorial_subjs/fsaverage/label/aparc.annot.ctab --a LeftTemporal_test --l labels/lh.middletemporal.label --l labels/lh.inferiortemporal.label --l labels/lh.superiortemporal.label sysname Linux hostname biowulf.nih.gov machine x86_64 user goldal2 subject fsaverage hemi lh SUBJECTS_DIR /data/EDAN/freesurfer/buckner_data/tutorial_subjs ColorTable /data/EDAN/freesurfer/buckner_data/tutorial_subjs/fsaverage/label/aparc.annot.ctab AnnotName LeftTemporal_test nlables 3 LabelThresh 0 0.000000 Loading /data/EDAN/freesurfer/buckner_data/tutorial_subjs/fsaverage/surf/lh.orig 1 2647065 bankssts 2 10511485 caudalanteriorcingulate 3 6500 caudalmiddlefrontal Mapping unhit to unknown Found 147704 unhit vertices Writing annot to /data/EDAN/freesurfer/buckner_data/tutorial_subjs/fsaverage/label/lh.LeftTemporal_test.annot Andrea Gold, Ph.D. Section on Development and Affective Neuroscience National Institute of Mental Health Room 201, Bldg. 15K, MSC 2670 Bethesda, MD 20892-2670 Phone: 301-827-9804 Fax: 301-402-2010 Email: andrea.gold(a)nih.gov<applewebdata://D38F487B-BA2B-4BF6-A9C4-96248AB2BE51/andrea.gold@nih.gov>

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Segmentation comparison between FS5.3 and FS6beta
by Matthieu Vanhoutte 15 Dec '15

15 Dec '15

Dear FS's experts, I have tried the recon-all process on one subject with both FS v5.3 and v6_beta. Although subcortical structures seems to be better segmented in v6_beta, I find that v6_beta over-segmented some other structures as cerebellum, hippocampus, ... I will attached in the FileDrop my T1.mgz, and aparc.a2009s+aseg.mgz files for both freesurfer versions. Could you please look at it and tell me what do you think about and advise me ? Thank you ! Best regards, Matthieu

4 10

R: Re: recon-all base error
by salvatoreandrea.92＠libero.it 15 Dec '15

15 Dec '15

I have 4 Gb, but I tried with a more poweful machine in the hospital and I got a similar error. I actually think there is a problem of alignment because the 3 T1s are quiet different from each other: they come from a patient affected by MS with a big lesion in the left frontal lobe. This lesion withdraws drastically in the last T1 as you can see from the two attachments. Moreover, I got a problem in the recon-all, given that freesurfer was not able to reconstruct properly the pial and white surfaces (the gray matter is spared in the patient, however it is not included in the lh.pial surf). Do you think there is a way to edit the brainmask for such a big lesion? Would this solve the problems with the recon-all base? Thank you! ----Messaggio originale---- Da: theniels(a)gmail.com Data: 15-dic-2015 9.31 A: "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] recon-all base error Hi - how much memory do you have on your machine? On Mon, Dec 14, 2015 at 10:54 AM, salvatoreandrea.92(a)libero.it <salvatoreandrea.92(a)libero.it> wrote: Hi Freesurfer experts! I tried to run recon-all base for a longitudinal analysis on my data. But I get the following error: Excessive topologic defect encountered: could not allocate 221309241 edges for retessellation Cannot allocate memory Linux salvatore-HP-630-Notebook-PC 3.19.0-39-generic #44~14.04.1-Ubuntu SMP Wed Dec 2 10:00:35 UTC 2015 x86_64 x86_64 x86_64 GNU/LinuxI tried with a more powerful pc but I encountered the same problem. Following further information: SUBJECT template_base DATE ven 11 dic 2015, 08.17.47, CET USER salvatore HOST salvatore-HP-630-Notebook-PC PROCESSOR x86_64 OS Linux Linux salvatore-HP-630-Notebook-PC 3.19.0-39-generic #44~14.04.1-Ubuntu SMP Wed Dec 2 10:00:35 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ /home/salvatore/freesurfer/bin/recon-all PWD /home/salvatore/freesurfer/subjects/template_base/scripts CMD mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 template_base lh _______________________________________________ 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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dmri_motion tracula timepoint to timepoint motion, or timepoint to reference?
by Ruth Carper 15 Dec '15

15 Dec '15

Hi, I'm hoping to use the dmri_motion tool to quantify motion for some diffusion data that did not use the eddy_correct tool. We have registration matrices that we've successfully reformatted, but I've been scanning the FreeSurfer forum and see some conflicting information about whether the input to dmri_motion should reflect registration of each time point to a single reference orregistration of each time point to the preceding time point. i.e. t0-t1, t0-t2, t0-t3, .... vs. t0-t1, t1-t2, t2-t3, ... What input does dmri_motion expect? I think it's the former but the confusion arises from this post: http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg41541.html5… ... Of our 4 motion measures, the rotation and translation are computed from the output of the eddy correction (which computes relative displacement from one volume to the next), and the intensity drop-out measures are computed from the raw uncorrected images (because the subsequent corrections will introduce some blurring and might lead to underestimation of the drop-out in each slice). So all measures are computed prior to B0 correction. Hope this helps, a.y But, the contents of the “eddy_correct” command appears to register each time point to a single reference time point. We’re using timepoint 1, i.e. b=0. From the text of Yendiki et al., 2013, I suspect that dmri_motion takes an input that is each timepoint to a single reference timepoint, but outputs a summary that is based on each timepoint to the immediately preceding timepoint? Can you clarify what input does dmri_motion expect? Thanks! Ruth Carper, PhDResearch Assistant Professor, SDSU

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TRACULA NaN values in stats files and empty stats file
by denizzgursel 15 Dec '15

15 Dec '15

Dear Tracula users, I reconstructed uncinate fasciculus using the latest version of Freesurfer and Tracula. However, there seems to be a problem with produced stats files in dpath folder . I have -nan values for the center_avg variables in the file "pathstats.overall.txt" and there is no entry at all for the file "pathstats.byvoxel.txt", it is basically empty. Do you know why this could be happened? Files look like this: pathstats.overall.txt Count 1500 Volume 35 Len_Min 35 Len_Max 35 Len_Avg 35 Len_Center 0 AD_Avg 0.000935047 AD_Avg_Weight 0.000935047 AD_Avg_Center -nan RD_Avg 0.000682719 RD_Avg_Weight 0.000682719 RD_Avg_Center -nan MD_Avg 0.000766828 MD_Avg_Weight 0.000766828 MD_Avg_Center -nan FA_Avg 0.224986 FA_Avg_Weight 0.224986 FA_Avg_Center -nan pathstats.byvoxel.txt # pathway start x y z AD RD MD FA AD_Avg RD_Avg MD_Avg FA_Avg # pathway end Thanks a lot for your help! -- D.

2 1

ERROR: Could not create directory
by jupiter 15 Dec '15

15 Dec '15

Hi, I am running freesurfer 6.0 beta with cuda 6.5 and FSL 5.0.9 on Linux platform, I've got following error: $ trac-all -path -c /scratchTRAC_TEST/dmrirc_first_exp_2.example ......... INFO: Found 8 baseline images (b = 0) out of a total of 136 frames INFO: Found 169534 voxels in brain mask INFO: Resolution of DWI space relative to base space is (1, 1, 1) Loading atlas reference volume from /scratch/TRAC_TEST/First_Exp/First_Exp_Tracula/JA/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz Loading affine registration from /scratch/TRAC_TEST/First_Exp/First_Exp_Tracula/JA/dmri/xfms/diff2mni.bbr.mat Loading segmentation map from /scratch/TRAC_TEST/First_Exp/First_Exp_Tracula/JA/dlabel/mni/aparc+aseg.nii.gz Creating output directory /scratch/TRAC_TEST/First_Exp/First_Exp_Tracula/JA/dpath/lh.cst_AS_avg33_mni_bbr ERROR: Could not create directory /scratch/TRAC_TEST/First_Exp/First_Exp_Tracula/JA/dpath/lh.cst_AS_avg33_mni_bbr Linux m2cvlnode17 2.6.32-504.16.2.el6.x86_64 #1 SMP Wed Apr 22 06:48:29 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux The directory /scratch/TRAC_TEST/First_Exp/First_Exp_Tracula/JA/dpath is fully acceptable, I even tried manually create the directory /scratch/TRAC_TEST/First_Exp/First_Exp_Tracula/JA/dpath/lh.cst_AS_avg33_mni_bbr, then run the command, it deleted /scratch/TRAC_TEST/First_Exp/First_Exp_Tracula/JA/dpath/lh.cst_AS_avg33_mni_bbr, and never created it even the message was "Creating output directory /scratch/TRAC_TEST/First_Exp/First_Exp_Tracula/JA/dpath/lh.cst_AS_avg33_mni_bbr". Could it be a bug or could it be some thing I am missing? Appreciate clues to fix it. Thank you. Kind regards, - ju

2 1

TRACULA preprocessing error
by denizzgursel 15 Dec '15

15 Dec '15

Dear all, I am running Tracula preprocessing on NIFTI files. After running the command: trac-all -prep -c I get the error: ... processing /data_august/Deniz/freesurfer/traculaoutput/DTI_con_AbSa90/dmri/dwi_tmp0032 mv -f /data_august/Deniz/freesurfer/traculaoutput/DTI_con_AbSa90/dmri/bvecs /data_august/Deniz/freesurfer/traculaoutput/DTI_con_AbSa90/dmri/bvecs.norot xfmrot /data_august/Deniz/freesurfer/traculaoutput/DTI_con_AbSa90/dmri/dwi.ecclog /data_august/Deniz/freesurfer/traculaoutput/DTI_con_AbSa90/dmri/bvecs.norot /data_august/Deniz/freesurfer/traculaoutput/DTI_con_AbSa90/dmri/bvecs ln -sf /data_august/Deniz/freesurfer/traculaoutput/DTI_con_AbSa90/dmri/dwi.nii.gz /data_august/Deniz/freesurfer/traculaoutput/DTI_con_AbSa90/dmri/data.nii.gz awk: fatal: cannot open file `1000' for reading (No such file or directory) mri_concat --i /data_august/Deniz/freesurfer/traculaoutput/DTI_con_AbSa90/dmri/dwi_frame.nii.gz --mean --o /data_august/Deniz/freesurfer/traculaoutput/DTI_con_AbSa90/dmri/lowb.nii.gz niiRead(): error opening file /data_august/Deniz/freesurfer/traculaoutput/DTI_con_AbSa90/dmri/dwi_frame.nii.gz ninputs = 1 Checking inputs ERROR: reading /data_august/Deniz/freesurfer/traculaoutput/DTI_con_AbSa90/dmri/dwi_frame.nii.gz Linux slow.mri.tu-muenchen.de 3.7.10-1.40-desktop #1 SMP PREEMPT Thu Jul 10 11:22:12 UTC 2014 (9b06319) x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Mon Nov 9 12:47:20 CET 2015 I checked the folder and 'dwi_frame.nii.gz' file was never created. I attached the trac-all.log file. Does anybody know how to solve this? Best, -- D.

3 4

Tracula - configuration file error
by L. Moreno-Lopez 15 Dec '15

15 Dec '15

Dear all, I am facing an error at the configuration file for trac-all. I am trying to run a single subject, for who there is a folder with all DWI DICOMs and a folder with the recon-all processing (Freesurfer 5.3). However, I am facing the following error, although no run list is specified. cs4$ export SUBJECTS_DIR=/scratch/lm618/tutorial_data/diffusion_recons cs4$ trac-all -prep -c /scratch/lm618/tutorial_data/diffusion_tutorial ERROR: run list is longer than subject list I'm attaching my configuration file. Any idea would be very much appreciate, Laura

2 1

Tracula Processing Question
by Douglas Merkitch 15 Dec '15

15 Dec '15

Hello FreeSurfer experts, We have a large dataset that was processed in FreeSurfer v 5.1 and we would like to run tracula on the dataset. Should we use the v 5.1 version of tracula to process the data? Or would it be acceptable/possible to use the v 5.3 tracula (with the v 5.1 processed T1 data)? Any advice or insight would be greatly appreciated! Thanks, Doug Douglas Merkitch Neurological Sciences Rush University Medical Center Email: Douglas_Merkitch(a)rush.edu<mailto:Douglas_Merkitch@rush.edu>

2 1

TRACULA question- pathstats not loading
by Golan, Noa 15 Dec '15

15 Dec '15

Hi, I am currently analyzing DTI data and I am having issues with one file in particular. When I run the tracheal -path -c step, all of the files are generated except the pathstats text files. Any thoughts? Thanks! Noa

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