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30099 discussions

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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searchable Destrieux atlas by recon all labels?
by Andrea Bozoki 11 Jan '16

11 Jan '16

Is there any interactive or searchable version of the Destrieux atlas parcellations (the ones used by aparc.a2009s.annot)? It would be very helpful to be able to toggle back and forth between individual recon-all labels and a color atlas of the relevant region when examining ROI-based quantitative output (output that is not visual). Thanks, Andrea B.

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BA46 volume from rostral mid-frontal gyrus
by Jae Cho 11 Jan '16

11 Jan '16

Dear FreeSurfer Experts, Could someone help me with a pipeline for creating a label from an edited existing label? I have aligned the aparc+aseg and its respective orig into ac-pc plane using AFNI. I then used fslmaths to make an ROI of just the rh_mid-frontal-gyrus. After editing the ROI using freeview, I am having trouble identifying which commands to use in order to create a new label and extracting the volume. Thank you, Jae

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About the pdf_gamma function in fsfast's toolbox
by LiTuX Sol 11 Jan '16

11 Jan '16

Hi, I’m working on some fMRI data processing these days. In order to construct a HRF, I find this Matlab function in fsfast. But after some careful comparison, it seems that the gamma pdf in this function is not consistent with FSL’s version, and differs from the standard gamma pdf. So perhaps it is a typo in your code? In this function, the gamma pdf is written as: > pdfx = (b.^2) .* (…); But comparing to FSL’s feat_model.cc, I think this term should be > pdfx = (b.^a) .*(…); Which will be consistent with the original gamma pdf from Wikipedia. Thanks for your nice software and thanks for your attention. 😊 Su, --- >From Beijing Normal University.

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Question about Intracranial Volume
by pietro de rossi 11 Jan '16

11 Jan '16

Dear FreeSurfers, I am editing a paper on subcortical volumes in deficit schizophrenia after some reviewers' comments. On of them suggested me to correct the volumes of subcortical structures for whole brain volume instead of intracranial volume. In the reviewer's opinion ICV estimated by FreeSurfer 5.1 has a bad quality and is not reliable. However, neither the reviewer provides any evidence, nor I could find any... Is there any evidence for this? Thanks in advance, Pietro -- Pietro De Rossi, MD ------------------------------------- Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma NESMOS Department (Neurosciences, Mental Health and Sensory Functions), School of Medicine and Psychology, Sapienza University, Sant’Andrea Hospital, Via di Grottarossa 1035-1039, 00189 Rome, Italy Laboratorio di Neuropsichiatria, Dipartimento di Neurologia Clinica e Comportamentale, IRCCS Fondazione Santa Lucia, via Ardeatina 306 - 00179 Roma Tel. +39 (0)6 51501358 Fax +39 (0)6 90280774 web: http://www.neuropsichiatrialab.com

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Hippocampal Subfields (6.0) Error
by Andrew Schoen 11 Jan '16

11 Jan '16

Hi all, We are running some hippocampal subfield segmentations for two independent studies. They have already been processed through the standard pipeline (5.3), so I was just running the following command: *recon-all -s ${subjectid} -hippocampal-subfields-T1* For both test cases, the processing seems to have halted (no more updates to the log file), but the command keeps running. For one study, it trailed off here: ************************************************************************************************************************ Resolution level 1 iteration 2 deformation iterations 13 Number of Meshes: 1 Using CG optimizer Did one deformation step of max. 0.00037944 voxels in 14.6033 seconds minLogLikelihoodTimesPrior = 2.3442e+06 Resolution level 1 iteration 2 deformation iterations 14 Number of Meshes: 1 Using CG optimizer Did one deformation step of max. 1.3541e-06 voxels in 3.5131 seconds minLogLikelihoodTimesPrior = 2.3442e+06 Resolution level 1 iteration 2 deformation iterations 15 Number of Meshes: 1 Using CG optimizer Did one deformation step of max. 0 voxels in 30.0807 seconds minLogLikelihoodTimesPrior = 2.3442e+06 maximalDeformation is too small; stopping Iteration 3 of 7 (eof) ************************************************************************************************************************ and the other here: ************************************************************************************************************************ Making Left-Accumbens-area map to reduced label 13 -------------- Making Unknown map to reduced label 14 Computing hyperparameters for estimation of Gaussians parameters Estimating typical intensities of molecular layer and alveus For ML in T1, we assume gray with high N In T2, we actually assume the same hypermean Smoothing mesh collection with kernel size 1.500000 ...Smoothing class: 0 Smoothing class: 1 Smoothing class: 2 Smoothing class: 3 Smoothing class: 4 Smoothing class: 5 Smoothing class: 6 Smoothing class: 7 Smoothing class: 8 Smoothing class: 9 Smoothing class: 10 Smoothing class: 11 Smoothing class: 12 Smoothing class: 13 done numberOfImages = 2 Image: 0 Image: 2 Iteration 1 of 7 (eof) ************************************************************************************************************************ Interestingly, for one study, we have T2-weighted images, and when I ran with that (same subject as second log, above), it ran to completion fine. Any idea what might be happening? Let me know if any other info would be useful! Thanks! Andrew Schoen Center for Healthy Minds Waisman Center University of Wisconsin - Madison

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