Freesurfer

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30084 discussions

registration errors in longitudinal analysis
by Lara Foland-Ross 13 Jan '16

13 Jan '16

Dear Freesurfer experts, I am working on a longitudinal analysis of cortical structure and am experiencing some errors with registration. I have 3 timepoints for each participant: time 1: age 2 time 2: age 5 time 3: age 10 Time 1 and 2 are from a 1.5T scanner. Time 3 is from a 3T scanner. Despite the age range and scanner difference, the registrations in the longitudinal pipeline (I'm using version 5.3) are performing relatively well. However, in comparing the LONG outputs slice by slice, it appears that in a majority of my subjects, there are some minor mismatches in brain anatomy. An example is attached here (minor_reg_error.jpg). In other instances, there are more substantial registration errors. Again, example attached here (major_reg_error.jpg). My question is how much mismatch is acceptable? And how can I go about fixing poor registrations in subjects who have significant errors in alignment? Many thanks in advance, Lara Lara Foland-Ross, Ph.D. Research Associate Center for Interdisciplinary Brain Sciences Research Stanford University School of Medicine 401 Quarry Road, Room 1356 Stanford, CA 94305-5795

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Re: [Freesurfer] recon-all issue
by Schell, Susanne 13 Jan '16

13 Jan '16

Dear Bruce, thanks for answering. The recon-all command lines we use is: recon-all -s subjectID -i /data/subjectID.nii.gz recon-all -s subjectID -all The files we used are 1) DICOM files 2) nii.gz files, but standard oriented and cut 3) nii.gz files When we look at the output pictures, they look different (see attached files) Greetings, Susanne ______________________________________ Susanne Schell, Dipl.-Psych. Sektion Störungen der Persönlichkeitsentwicklung Klinik für Kinder- und Jugendpsychiatrie Universitätsklinikum Heidelberg Tel: (+49) - (0)6221-56 35135 e-mail: susanne.schell(a)med.uni-heidelberg.de<mailto:susanne.schell@med.uni-heidelberg.de>

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propagating edits across in the FreeSurfer longitudinal stream
by Collins, Jessica Ann 13 Jan '16

13 Jan '16

Dear FS Community, I am currently using FreeSurfer 5.3 to conduct a longitudinal analysis of atrophy in Semantic Dementia. Because of the profound temporal pole atrophy in these patients, I have been making a lot of manual edits (mostly control points and wm edits) to the baseline scan, and these edits are often consistent across different time points for the same individual. I understand that with the longitudinal stream it is necessary to make edits to all cross-sectional scans, however I was wondering if there was any way to propagate manual edits made at one time point to future time points for the same subject? Any insight would be appreciated! Best regards, Jessica Jessica Collins, Ph.D. Postdoctoral Research Fellow Department of Neurology MGH-Harvard Medical School

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mri_convert error (dicom to nifti)
by Retzepi, Kallirroi 12 Jan '16

12 Jan '16

Hi, I am running mri_convert (from .dcm to .nii.gz) and I get the following error: ERROR: RLL-encoded image data not supported! (Transfer Syntax UID: 1.2.840.10008.1.2.5) Any help is appreciated. Thank you! Kalli

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(no subject)
by Smaragdi A. 12 Jan '16

12 Jan '16

Hi mailing list, I have encountered this problem in Freesurfer a number of times now and I wondered if any of you had any solutions. It seems that sometimes after a recon-all has been run, there is a large overlap of the pial boundary and wm boundary, in the same region each time near the lateral ventricles (it can be on either hemisphere or both). I have attached a print screen of the issue, this time in the LH. As you can see, we have tried adding CPs and have also added WM, but after re-running it, the problem still exists. We have also tried running the randomness, but this has had no effect. Any suggestions as to what we could do to fix this would be great - thank you!

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Re: [Freesurfer] recon-all issue
by Schell, Susanne 12 Jan '16

12 Jan '16

Dear colleagues, as I posted before, we are recently using the freesurfer recon-all command. Here are three different commands we used: 1)# Version 1: Import as DICOM #!/bin/sh -e # Segmentierung mit FreeSurfer. # Die Ergebnisse werden in dem Verzeichnis gespeichert, in dem sich # dieses Script befindet. # Verzeichnis der DICOM Daten DCMDIR=../../Daten/DICOM # Verzeichnis der NIFTI Daten NIIDIR=../../Daten/NIFTI # Unterverzeichnis der T1 Daten T1DIR=E010Kopf_Studie/M_MPRAGE_sag cd `dirname $0` export SUBJECTS_DIR=`pwd` for i in $DCMDIR/3001* ; do ID=`basename $i` if [ ! -d $i/$T1DIR ] ; then echo "*** $ID: T1 DICOM Bilder nicht gefunden." continue fi if [ -f $ID/scripts/IsRunning.lh+rh ] ; then cat $ID/scripts/IsRunning.lh+rh echo "*** $ID: Segmentierung lÃ¤uft gerade oder wurde abgebrochen." echo "*** $ID: Bei Abbruch '$ID/scripts/IsRunning.lh+rh' lÃ¶schen." continue fi if [ ! -f $SUBJECTS_DIR/$ID/mri/orig/001.mgz ] ; then recon-all -s $ID -i $i/$T1DIR/IM-*-0001.dcm fi if ! grep -q "CMDARGS -s $ID -all" \ $SUBJECTS_DIR/$ID/scripts/recon-all.done ; then recon-all -s $ID -all fi done 2)# Version 2: Import as NIFTI in standard orientation #!/bin/sh -e # Segmentierung mit FreeSurfer. # Die Ergebnisse werden in dem Verzeichnis gespeichert, in dem sich # dieses Script befindet. # Verzeichnis der DICOM Daten DCMDIR=../../Daten/DICOM # Verzeichnis der NIFTI Daten NIIDIR=../../Daten/NIFTI cd `dirname $0` export SUBJECTS_DIR=`pwd` for i in $NIIDIR/3001*/*_T1_fov.nii.gz ; do DIR=`dirname $i` ID=`basename $DIR` if [ -f $ID/scripts/IsRunning.lh+rh ] ; then cat $ID/scripts/IsRunning.lh+rh echo "*** $ID: Segmentierung lÃ¤uft gerade oder wurde abgebrochen." echo "*** $ID: Bei Abbruch '$ID/scripts/IsRunning.lh+rh' lÃ¶schen." continue fi if [ ! -f $SUBJECTS_DIR/${ID}_2/mri/orig/001.mgz ] ; then recon-all -s ${ID}_2 -i $i fi if ! grep -q "CMDARGS -s ${ID}_2 -all" \ $SUBJECTS_DIR/${ID}_2/scripts/recon-all.done ; then recon-all -s ${ID}_2 -all fi done 3) # Version 3: Import as NIFTI.gz #!/bin/sh -e # Segmentierung mit FreeSurfer. # Die Ergebnisse werden in dem Verzeichnis gespeichert, in dem sich # dieses Script befindet. # Verzeichnis der DICOM Daten DCMDIR=../../Daten/DICOM # Verzeichnis der NIFTI Daten NIIDIR=../../Daten/NIFTI cd `dirname $0` export SUBJECTS_DIR=`pwd` for i in $NIIDIR/3001*/*_T1.nii.gz ; do DIR=`dirname $i` ID=`basename $DIR` if [ -f $ID/scripts/IsRunning.lh+rh ] ; then cat $ID/scripts/IsRunning.lh+rh echo "*** $ID: Segmentierung lÃ¤uft gerade oder wurde abgebrochen." echo "*** $ID: Bei Abbruch '$ID/scripts/IsRunning.lh+rh' lÃ¶schen." continue fi if [ ! -f $SUBJECTS_DIR/${ID}_3/mri/orig/001.mgz ] ; then recon-all -s ${ID}_3 -i $i fi if ! grep -q "CMDARGS -s ${ID}_3 -all" \ $SUBJECTS_DIR/${ID}_3/scripts/recon-all.done ; then recon-all -s ${ID}_3 -all fi done If you just look at the different output files, they look slightly different (just by looking at it). Maybe you can help us by trying to find out why the output files are different? Thanks very much in advance! Best regards, Susanne ______________________________________ Susanne Schell, Dipl.-Psych. Sektion Störungen der Persönlichkeitsentwicklung Klinik für Kinder- und Jugendpsychiatrie Universitätsklinikum Heidelberg Tel: (+49) - (0)6221-56 35135 e-mail: susanne.schell(a)med.uni-heidelberg.de

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Calculating new volumes
by Julio Alberto González Torre 12 Jan '16

12 Jan '16

Hi Freesurfer experts. Is there any tool to perfom volume calculations? Such binarize a volume, intersect two volumes, sum volumes etc? Thanks.

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R: R: Re: FDR correction
by stdp82＠virgilio.it 11 Jan '16

11 Jan '16

Hi list, I have resolved my issue on the previous point 2 by downloading matlab file on: https://sites.google.com/site/kittipat/mvpa-for-brain- fmri/convert_matlab_nifti after the command that you suggesedt: fdrthresh = fast_fdrthresh(p,0.05); the script produce p=0.053 Therefore, coming back to my answer I guess that no setting of the FDR threshold to 0.05/3 is requested in order to correct for multiple comparison (right and left hemispheres + subcortical). Is it correct? On the previous point 4 my answer remains open. I have used this command line: mri_surfcluster --in sig.nii.gz --hemi rh --sign abs --no-adjust --fdr 0.05 -- minarea 5 --sum summaryfile --subject fsaverage --annot aparc but I have difficulty to undestand which is the option to visualize the map corrected by mri_surfcluster. Additionally, from --help I do not understand the use of --ocn and --cst options. Best regards, Stefano >>----Messaggio originale---- >>Da: stdp82(a)virgilio.it >>Data: 7-gen-2016 15.40 >>A: <freesurfer(a)nmr.mgh.harvard.edu> >>Ogg: [Freesurfer] R: Re: FDR correction >> >>Thanks. >> >>- on question 2: >>I have run >>rh = MRIread('sig.mgh'); >>but this error occur >>Undefined function 'MRIread' for input arguments of type 'char'. >>no help is permitted on MRIread >> >>-on question 3: >>I'm using this command line to visualize the map describing the functional >>connectivity form seed to cortex >> >>tksurfer fsaverage rh inflated -aparc -overlay R_seed/my-glm.wls/group. >>diff/sig.nii.gz -fminmax 1.3 3 >>tksurfer fsaverage lh inflated -aparc -overlay L_seed/my-glm.wls/group. >>diff/sig.nii.gz -fminmax 1.3 3 >> >>in this way I visualize correctly for right and left hemisphere the >>connectivity from ipsilateral seed. >>If I would visualize the the connectivity from contralateral seed, how can I >>do? >> >>If I use >>tksurfer fsaverage lh inflated -aparc -overlay R_seed/my-glm.wls/group. >>diff/sig.nii.gz -fminmax 1.3 3 >>tksurfer fsaverage rh inflated -aparc -overlay L_seed/my-glm.wls/group. >>diff/sig.nii.gz -fminmax 1.3 3t >> >>-on question 4: >>I have resolved with this command line: >>mri_surfcluster --in sig.nii.gz --hemi rh --sign abs --no-adjust --fdr 0.05 >-- >>minarea 5 --sum summaryfile --subject fsaverage --annot aparc >> >>but I have difficulty to undestand which is the option to visualize the map >>corrected by mri_surfcluster. >>Additionally, from --help I do not understand the use of --ocn and --cst >>options. >> >>Best regards, >> >> >>Stefano >> >> >> >> >> >>>----Messaggio originale---- >>>Da: greve(a)nmr.mgh.harvard.edu >>>Data: 7-gen-2016 0.34 >>>A: <freesurfer(a)nmr.mgh.harvard.edu> >>>Ogg: Re: [Freesurfer] FDR correction >>> >>> >>> >>>On 01/06/2016 11:00 AM, stdp82(a)virgilio.it wrote: >>>> Hi list, >>>> >>>> I would like to ask you a number of questions regarding the FDR which >>>> is performed following seed-based fcMRI using FS-FAST. >>>> 1-In the previous mail you have suggested me to use mir_fdr command >>>> line (version 6.0). Because I have some problem with new version >>>> license (as reported in previous mail) and, overall I have run my data >>>> using version 5.3, I would ask you whether FDR integrated in tksurfer >>>> (version 5.3) is however reliable as the FDR included in 6.0? >>>Yes, they call the same code. >>>> >>>> 2-Becouse the FDR analysis was performed separately for the right and >>>> left hemispheres and the subcortical structures, should I set the FDR >>>> threshold to 0.05/3 in order to correct for multiple comparison? (I >>>> have one group) >>>I'm not sure. You can try to run both hemispheres in matlab, somethiing like >>>lh = MRIread('sig.lh.mgh'); >>>lhp = 10^-abs(lh.vol); >>>rh = MRIread('sig.rh.mgh'); >>>rlhp = 10^-abs(rh.vol); >>> >>>p = [lhp rhp]; >>>fdrthresh = fast_fdrthresh(p,fdr); >>> >>>> >>>> 3- Is easy for me to follow the guidelines and visualize the cortical >>>> areas which are functionally connected with the omolateral seed. How >>>> can I do to visualize also the the cortical areas which are >>>> functionally connected with the controlateral seed? If change only the >>>> rh/lh in command line the visualization of the results is wrong. >>>I don't understand. >>>> >>>> 4- I'd like to perform mri_surfcluster on a group to eliminate cluster >>>> < 5 >>>> voxels from sig.nii.gz after FDR correction. I'm running >>>> mri_surfcluster --in >>>> sig.nii.gz --hemi rh --sign abs --fdr 0.05 --minarea 5 --sum >>>> summaryfile --ocn >>>> ocnid >>>> but --subject ... must be included. >>>> How should do I do? I would like to run my analysis on group results, >>>> not on a single subject. >>>If this is from a group analysis, the subject is probablly fsaverage >>>> >>>> Thanks for your work. >>>> 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 >> >

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fMRI activation color inversion
by Hirsch, Gabriella 11 Jan '16

11 Jan '16

Hi FreeSurfer experts, I recently ran a simple fMRI analysis in FSL and now generating images of the activation in freesurfer using reg-feat2anat to register the functional activation to the freesurfer recon-all files, and generating the images using tksurfer: tksurfer pilot_3 lh inflated -annot aparc.annot -ov run4578_COMB.gfeat/cope1.feat/stats/zstat1.nii.gz -ovreg run4_fwhm8.feat/reg/freesurfer/anat2std.register.dat -fthresh 4 -fslope 1 However I have come across a strange occurrence when I change the threshold. Specifically, when I set the -fthresh flag (bolded) as 4 (i.e. p=0.0001) or less, the activation colors comes off as they should (see 4_blue attached) in terms of how I set up the contrasts. But when I set my threshold to 5 or higher (changing nothing else), the colors of the activation invert (see 5_red attached). What does this mean? How can I fix this? Any ideas would be greatly appreciated! Thank you! Gabriella Mass. Eye and Ear Confidentiality Notice: This e-mail and any files transmitted with it are confidential and are intended solely for the use of the individual(s) addressed in the message above. This communication may contain sensitive or confidential information. If you are not an intended recipient, dissemination, forwarding, printing, or copying of this e-mail is strictly prohibited. If you believe you have received this e-mail in error and the email contains patient information, please contact the Mass. Eye and Ear Compliance Line at 617-263-1600. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and delete the e-mail.

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PET processing seg fault with mri_glmfit --mrtm1
by Jonathan DuBois 11 Jan '16

11 Jan '16

Hi Freesurfer developers, I’m trying to perform BP analysis with mri_glmfit —mrtm1. I ran mri_gtmpvc without PVC, which finished without error. However, the km.hb.tac.nii.gz appears empty when I open it with fslview or tkmedit, although this may be due to the nature of the file (I’m not sure what it is supposed to show). The km.ref.tac.dat and km.hb.tac.dat are normal. Please let me know what you think. The command and error: mri_glmfit --y km.hb.tac.nii.gz --mrtm1 km.ref.tac.dat time.dat --o mrtm1 --no-est-fwhm --nii.gz Segmentation fault (core dumped) Where time.dat is a text file with the time (in seconds) of each frame: 0 30 60 90 120 150 180 240 300 360 420 540 660 780 900 1020 1140 1260 1380 1620 1860 2100 2400 2700 3000 3300 I’m using the linux version 6 beta downloaded on Oct. 30th freesurfer-Linux-centos4_x86_64-dev-20151030 Best, Jonathan

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