Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

Hippocampal mask from the subfields masks
by Ole Johan Evjenth Sørhaug 21 Aug '19

21 Aug '19

External Email - Use Caution Dear freesurfer experts, I wish to use the subfield segmentations from the 6.0 version of freesurfer to have a segmentation of the whole hippocampus. As far as I have understood, a segmentation of the whole hippocampus is not provided by default by the subfields module. Would the correct way to obtain this be by using the command mri_mergelabels on the subfield segmentations, then use mri_label2vol to create an mgz volume of the whole hippocampus? Regards Ole Johan Evjenth Sørhaug

1 0

Re-running lGI flag
by Avi Gharehgazlou 20 Aug '19

20 Aug '19

External Email - Use Caution Hi, I have a very quick question... I've ran the lGI flag (-localGI) on my participants. However, I've then performed manual edits (i.e. control points, etc) on some participants and re-ran recon-all and lGI flag after my edits.. To be sure, I want to re-run the lGI flag (-localGI) on all my participants again before performing statistical analysis (because I've been working on this data for a while now and want to make sure I have ran the lGI flag on all edited and final cortices before stats and that I haven't missed anyone by accident). I wanted to ask if this would be okay? I mean, would it be okay to run lGI for a brain that I may have already ran the lGI flag on? Or do I have to delete anything before doing so? I would really appreciate your reply, Thank you so much, Avi

1 0

mris_label2annot gives wrong label
by Rachel S 20 Aug '19

20 Aug '19

External Email - Use Caution Hi Freesurfer community, I was trying to use mris_label2annot to generate annotation file, my commands are: mris_label2annot --s p6 --h rh --a t500 --ldir $SUBJECTS_DIR/p6/label/regenerated_rh_500 --nhits nhits.mgh --ctab /home/rachelsun/Software/freesurfer/resolution1015_LUT.txt --l $SUBJECTS_DIR/p6/label/regenerated_rh_500/rh.pericalcarine_7.label --surf pial The output of the command is: Reading ctab /home/rachelsun/Software/freesurfer/resolution1015_LUT.txt Number of ctab entries 1016 $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ cwd /home/rachelsun/Software/freesurfer/subjects/fsaverage5/mri cmdline mris_label2annot --s p6 --h rh --a t500 --ldir /home/rachelsun/Software/freesurfer/subjects/p6/label/regenerated_rh_500 --nhits nhits.mgh --ctab /home/rachelsun/Software/freesurfer/resolution1015_LUT.txt --l /home/rachelsun/Software/freesurfer/subjects/p6/label/regenerated_rh_500/rh.pericalcarine_7.label --surf pial sysname Linux hostname rachel-pc machine x86_64 user rachelsun subject p6 hemi rh SUBJECTS_DIR /home/rachelsun/Software/freesurfer/subjects ColorTable /home/rachelsun/Software/freesurfer/resolution1015_LUT.txt AnnotName t500 NHitsFile nhits.mgh nlables 1 LabelThresh 0 0.000000 Loading /home/rachelsun/Software/freesurfer/subjects/p6/surf/rh.pial 1 107939 rh.lateralorbitofrontal_9 Mapping unhit to unknown Found 123130 unhit vertices Writing annot to /home/rachelsun/Software/freesurfer/subjects/p6/label/rh.t500.annot I am sure I have rh.pericalcarine_7 in the folder, but the code always generates rh.lateralorbitofrontal_9 region. And I also attached my colortable file for your reference. Thank you for your help. Best regards, Rachel

2 4

BIDS Steering Group nominations
by Franklin Feingold 19 Aug '19

19 Aug '19

External Email - Use Caution Hi FreeSurfer! We are announcing the nomination period for our fellow colleagues (or self-nomination) to the BIDS Steering Group! The BIDS Steering Group is proposed within our governance document<https://docs.google.com/document/d/1R-J2lL9V_wIkYhye4zH-feyl4P4J8NyO40rIYyY…>. This group is charged with preserving the longevity and sustainability of the BIDS standard. This will be a 5 person group that represents different modalities and perspectives. To nominate please fill out this form<https://forms.gle/scwDrFJHTiddyVMG6>. We will be running the nominations until August 28 at 11:59pm PST. Thank you! Franklin

1 0

mri_robust_template in FMRIprep rotation should not scale error
by Dylan Nielson 19 Aug '19

19 Aug '19

External Email - Use Caution Hi Freesurfer folks, I'm running Freesurfer's longitudinal pipeline as part of FMRIprep and I've got two subjects generating similar errors in the mri_robust_template step, one of which I've copied below. I've defaced these subjects and saved the working directories so I can share them with you on the ftp site if you'd like. Thanks for your help, Dylan Nielson Error for subject 22477: RuntimeError: Command: mri_robust_template --satit --mov /lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-22477_ses-01_acq-mprage_rec-ORIG_run-1_T1w_ras_corrected.nii.gz /lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1/sub-22477_ses-02_acq-mprage_rec-ORIG_run-1_T1w_ras_corrected.nii.gz /lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct2/sub-22477_ses-03_acq-mprage_rec-ORIG_run-1_T1w_ras_corrected.nii.gz /lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct3/sub-22477_ses-04_acq-mprageABCD_rec-ORIG_run-1_T1w_corrected.nii.gz --inittp 1 --iscale --template sub-22477_ses-01_acq-mprage_rec-ORIG_run-1_T1w_ras_template.nii.gz --subsample 200 --lta /lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/t1_merge/tp1.lta /lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/t1_merge/tp2.lta /lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/t1_merge/tp3.lta /lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/t1_merge/tp4.lta Standard output: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ --satit: Will estimate SAT iteratively! --mov: Using /lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-22477_ses-01_acq-mprage_rec-ORIG_run-1_T1w_ras_corrected.nii.gz as movable/source volume. --mov: Using /lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1/sub-22477_ses-02_acq-mprage_rec-ORIG_run-1_T1w_ras_corrected.nii.gz as movable/source volume. --mov: Using /lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct2/sub-22477_ses-03_acq-mprage_rec-ORIG_run-1_T1w_ras_corrected.nii.gz as movable/source volume. --mov: Using /lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct3/sub-22477_ses-04_acq-mprageABCD_rec-ORIG_run-1_T1w_corrected.nii.gz as movable/source volume. Total: 4 input volumes --inittp: Using TP 1 as target for initialization --iscale: Enableing intensity scaling! --template: Using sub-22477_ses-01_acq-mprage_rec-ORIG_run-1_T1w_ras_template.nii.gz as template output volume. --subsample: Will subsample if size is larger than 200 on all axes! --lta: Will output LTA transforms Setting iscale ... reading source '/lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-22477_ses-01_acq-mprage_rec-ORIG_run-1_T1w_ras_corrected.nii.gz'... converting source '/lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-22477_ses-01_acq-mprage_rec-ORIG_run-1_T1w_ras_corrected.nii.gz' to bspline ... MRItoBSpline degree 3 reading source '/lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1/sub-22477_ses-02_acq-mprage_rec-ORIG_run-1_T1w_ras_corrected.nii.gz'... converting source '/lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1/sub-22477_ses-02_acq-mprage_rec-ORIG_run-1_T1w_ras_corrected.nii.gz' to bspline ... MRItoBSpline degree 3 reading source '/lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct2/sub-22477_ses-03_acq-mprage_rec-ORIG_run-1_T1w_ras_corrected.nii.gz'... converting source '/lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct2/sub-22477_ses-03_acq-mprage_rec-ORIG_run-1_T1w_ras_corrected.nii.gz' to bspline ... MRItoBSpline degree 3 reading source '/lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct3/sub-22477_ses-04_acq-mprageABCD_rec-ORIG_run-1_T1w_corrected.nii.gz'... converting source '/lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct3/sub-22477_ses-04_acq-mprageABCD_rec-ORIG_run-1_T1w_corrected.nii.gz' to bspline ... MRItoBSpline degree 3 MultiRegistration::initializing Xforms (init 1 , maxres 0 , iterate 5 , epsit 0.01 ) : [init] ========================= TP 2 to TP 1 ============================== Register TP 2 ( /lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1/sub-22477_ses-02_acq-mprage_rec-ORIG_run-1_T1w_ras_corrected.nii.gz ) to TP 1 ( /lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-22477_ses-01_acq-mprage_rec-ORIG_run-1_T1w_ras_corrected.nii.gz ) [init] ========================= TP 4 to TP 1 ============================== Register TP 4 ( /lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct3/sub-22477_ses-04_acq-mprageABCD_rec-ORIG_run-1_T1w_corrected.nii.gz ) to TP 1 ( /lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-22477_ses-01_acq-mprage_rec-ORIG_run-1_T1w_ras_corrected.nii.gz ) [init] ========================= TP 3 to TP 1 ============================== Register TP 3 ( /lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct2/sub-22477_ses-03_acq-mprage_rec-ORIG_run-1_T1w_ras_corrected.nii.gz ) to TP 1 ( /lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-22477_ses-01_acq-mprage_rec-ORIG_run-1_T1w_ras_corrected.nii.gz ) - Max Resolution used: 2 -- gpS ( 51 , 64 , 64 ) -- gpT ( 51 , 64 , 64 ) - running loop to estimate saturation parameter: - Max Resolution used: 2 -- gpS ( 51 , 64 , 64 ) -- gpT ( 51 , 64 , 64 ) - running loop to estimate saturation parameter: - Max Resolution used: 2 -- gpS ( 51 , 64 , 64 ) -- gpT ( 51 , 64 , 64 ) - running loop to estimate saturation parameter: * WARNING: TP 2 to 1 did not converge !! * WARNING: TP 3 to 1 did not converge !! * WARNING: TP 4 to 1 did not converge !! Input rotation's max deviation from rotation is: 6.17523e-05 computing mean coord of TP 1 ( /lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-22477_ses-01_acq-mprage_rec-ORIG_run-1_T1w_ras_corrected.nii.gz ) mapping back to rot, err = 1.92296e-16 computing mean coord of TP 2 ( /lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1/sub-22477_ses-02_acq-mprage_rec-ORIG_run-1_T1w_ras_corrected.nii.gz ) mapping back to rot, err = 5.2975e-15 computing mean coord of TP 3 ( /lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct2/sub-22477_ses-03_acq-mprage_rec-ORIG_run-1_T1w_ras_corrected.nii.gz ) mapping back to rot, err = 7.55033e-16 computing mean coord of TP 4 ( /lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct3/sub-22477_ses-04_acq-mprageABCD_rec-ORIG_run-1_T1w_corrected.nii.gz ) Standard error:Internal Error for tp 3 -> template Rotation should not scale ( 3.08776e-05 ) Debug Info: A = [ ... 0.9969922338242 -0.0778269037878 0.0033377292333 0.0777901549173 0.9969203604879 0.0099370478686 -0.0041009199390 -0.0096472102695 0.9999450558122 ] R = [ ... 0.9969614041457 -0.0778255626866 0.0033377292333 0.0777890868352 0.9969203142925 0.0099370478686 -0.0041008064181 -0.0096472142869 0.9999450558122 ] S = [ ... 1.0000308195503 -0.0000013334491 -0.0000000000000 -0.0000013334491 1.0000001503863 0.0000000000000 -0.0000000000000 0.0000000000000 1.0000000000000 ] Internal Error: Rotation should not scale. Return code: 248 Error for subject 24028: Traceback (most recent call last): File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 69, in run_node result['result'] = node.run(updatehash=updatehash) File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 472, in run result = self._run_interface(execute=True) File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 563, in _run_interface return self._run_command(execute) File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 643, in _run_command result = self._interface.run(cwd=outdir) File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/freesurfer/base.py", line 265, in run return super(FSCommandOpenMP, self).run(**inputs) File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/freesurfer/base.py", line 144, in run return super(FSCommand, self).run(**inputs) File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 375, in run runtime = self._run_interface(runtime) File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 758, in _run_interface self.raise_exception(runtime) File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 695, in raise_exception ).format(**runtime.dictcopy())) RuntimeError: Command: mri_robust_template --satit --mov /lscratch/33514484/wrk/fmriprep_wf/single_subject_24028_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-24028_ses-01_acq-mprage_rec-ORIG_run-1_T1w_corrected.nii.gz /lscratch/33514484/wrk/fmriprep_wf/single_subject_24028_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1/sub-24028_ses-02_acq-mprage_rec-ORIG_run-1_T1w_corrected.nii.gz --inittp 1 --iscale --template sub-24028_ses-01_acq-mprage_rec-ORIG_run-1_T1w_template.nii.gz --subsample 200 --lta /lscratch/33514484/wrk/fmriprep_wf/single_subject_24028_wf/anat_preproc_wf/anat_template_wf/t1_merge/tp1.lta /lscratch/33514484/wrk/fmriprep_wf/single_subject_24028_wf/anat_preproc_wf/anat_template_wf/t1_merge/tp2.lta Standard output: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ --satit: Will estimate SAT iteratively! --mov: Using /lscratch/33514484/wrk/fmriprep_wf/single_subject_24028_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-24028_ses-01_acq-mprage_rec-ORIG_run-1_T1w_corrected.nii.gz as movable/source volume. --mov: Using /lscratch/33514484/wrk/fmriprep_wf/single_subject_24028_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1/sub-24028_ses-02_acq-mprage_rec-ORIG_run-1_T1w_corrected.nii.gz as movable/source volume. Total: 2 input volumes --inittp: Using TP 1 as target for initialization --iscale: Enableing intensity scaling! --template: Using sub-24028_ses-01_acq-mprage_rec-ORIG_run-1_T1w_template.nii.gz as template output volume. --subsample: Will subsample if size is larger than 200 on all axes! --lta: Will output LTA transforms Setting iscale ... reading source '/lscratch/33514484/wrk/fmriprep_wf/single_subject_24028_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-24028_ses-01_acq-mprage_rec-ORIG_run-1_T1w_corrected.nii.gz'... converting source '/lscratch/33514484/wrk/fmriprep_wf/single_subject_24028_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-24028_ses-01_acq-mprage_rec-ORIG_run-1_T1w_corrected.nii.gz' to bspline ... MRItoBSpline degree 3 reading source '/lscratch/33514484/wrk/fmriprep_wf/single_subject_24028_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1/sub-24028_ses-02_acq-mprage_rec-ORIG_run-1_T1w_corrected.nii.gz'... converting source '/lscratch/33514484/wrk/fmriprep_wf/single_subject_24028_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1/sub-24028_ses-02_acq-mprage_rec-ORIG_run-1_T1w_corrected.nii.gz' to bspline ... MRItoBSpline degree 3 MultiRegistration::initializing Xforms (init 1 , maxres 0 , iterate 5 , epsit 0.01 ) : [init] ========================= TP 2 to TP 1 ============================== Register TP 2 ( /lscratch/33514484/wrk/fmriprep_wf/single_subject_24028_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1/sub-24028_ses-02_acq-mprage_rec-ORIG_run-1_T1w_corrected.nii.gz ) to TP 1 ( /lscratch/33514484/wrk/fmriprep_wf/single_subject_24028_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-24028_ses-01_acq-mprage_rec-ORIG_run-1_T1w_corrected.nii.gz ) - Max Resolution used: 2 -- gpS ( 43 , 64 , 64 ) -- gpT ( 43 , 64 , 64 ) - running loop to estimate saturation parameter: * WARNING: TP 2 to 1 did not converge !! Input rotation's max deviation from rotation is: 4.27526e-05 computing mean coord of TP 1 ( /lscratch/33514484/wrk/fmriprep_wf/single_subject_24028_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-24028_ses-01_acq-mprage_rec-ORIG_run-1_T1w_corrected.nii.gz ) mapping back to rot, err = 0 computing mean coord of TP 2 ( /lscratch/33514484/wrk/fmriprep_wf/single_subject_24028_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1/sub-24028_ses-02_acq-mprage_rec-ORIG_run-1_T1w_corrected.nii.gz ) Standard error:Internal Error for tp 1 -> template Rotation should not scale ( 2.13756e-05 ) Debug Info: A = [ ... 0.9976866765353 0.0613358758176 0.0285823594087 -0.0624208989520 0.9972963115456 0.0387788304011 -0.0261239538328 -0.0404768298397 0.9988387368875 ] R = [ ... 0.9977078546957 0.0613362673314 0.0285814448261 -0.0624218986995 0.9972961437200 0.0387802563678 -0.0261255285353 -0.0404754744389 0.9988389223132 ] S = [ ... 0.9999787668370 -0.0000003656818 0.0000010063421 -0.0000003656818 1.0000001982183 -0.0000013585088 0.0000010063421 -0.0000013585088 0.9999997856304 ] Internal Error: Rotation should not scale. Return code: 248

3 5

help for calculating the correlation
by tange_neuro 19 Aug '19

19 Aug '19

External Email - Use Caution Hi all, I am deeply confused and terribly needed some help, and I failed to find the answer in the Freesurfer website. I had two patient groups F and R. To analysis the correlation between active time and cortical thickness, I tried two different methods A and B (A, treating patients in different group F and R as shown in attached figure A; B, treating all patients as one group FR as shown in attached figure B), and got distinctly different results. So, my questions: 1、Which one is actually correct for calculating the correlation between active time and thickness, and what does the other one mean? 2、Does "--cache 3 abs --cwp 0.999" means that the result is only corrected with vertex level P < 0.001, and no cluster level correction is conducted? I am looking forward to getting your help. Sincerely yours, Ge Tan

2 2

autorecon3 with T2_min parameter
by Marco Aqil 19 Aug '19

19 Aug '19

External Email - Use Caution ?Hi, When calling recon-all autorecon3, with the -T2pial flag, and a -T2_min value specified via expert options file, I noticed that this parameter is passed to the first call of mris_make_surfaces, which looks, for example, as follows: ---------------- #@# Make Pial Surf lh Mon Aug 19 13:43:02 CEST 2019 <scripts folder path> mris_make_surfaces -save-res -save-target -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs -T2_min 35 sub-006 lh ---------------- However, the second call of mris_make_surfaces, which relies on T2 data to refine the pial, does not receive the T2_min parameter, and looks as follows: --------------- #@# Refine Pial Surfs w/ T2/FLAIR Mon Aug 19 14:02:23 CEST 2019 <other T2 pial steps> mris_make_surfaces -save-res -save-target -orig_white white -orig_pial woT2.pial -aseg ../mri/aseg.presurf -nowhite -mgz -T1 brain.finalsurfs -T2 ../mri/T2 -nsigma_above 2 -nsigma_below 5 sub-006 lh --------------- Is this the expected behavior, or should the T2_min be passed to the second call as well? In case it is needed, I am using freesurfer-dev, version obtained on july 11th. Thank you very much. Best, Marco?

1 0

question about qdec
by 310913949 19 Aug '19

19 Aug '19

External Email - Use Caution Hi FS Experts, I meet some problem when I use QDEC for Group analysis. When I click Generate Stats Data Tables, it report the errors as follows: dec/gender.levels Female Male done. Reading discrete factor levels from config file /usr/local/freesurfer/subjects/qdec/diagnosis.levels TLE extra_TLE done. Data table /usr/local/freesurfer/subjects/qdec/qdec.table.dat loaded. Verifying subject data.sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'PT1_01' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'PT1_03' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'PT1_04' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'PT1_06' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'PT1_11' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'PT1_12' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'PT1_14' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'PT1_47' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'PT1_55' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'PT1_05' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'PT1_16' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'PT1_18' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'PT1_20' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'PT1_23' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'PT1_24' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'PT1_40' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'PT1_75' in SUBJECTS_DIR Input table: /usr/local/freesurfer/subjects/qdec/qdec.table.dat Subj#, SubjID, Data... 1 PT1_01 Female 23.000000 TLE 2 PT1_03 Male 38.000000 TLE 3 PT1_04 Male 26.000000 TLE 4 PT1_06 Female 45.000000 TLE 5 PT1_11 Female 20.000000 TLE 6 PT1_12 Male 23.000000 TLE 7 PT1_14 Female 39.000000 TLE 8 PT1_47 Female 30.000000 TLE 9 PT1_55 Female 22.000000 TLE 10 PT1_05 Male 42.000000 extra_TLE 11 PT1_16 Female 34.000000 extra_TLE 12 PT1_18 Male 30.000000 extra_TLE 13 PT1_20 Male 40.000000 extra_TLE 14 PT1_23 Male 30.000000 extra_TLE 15 PT1_24 Female 29.000000 extra_TLE 16 PT1_40 Male 30.000000 extra_TLE 17 PT1_75 Female 24.000000 extra_TLE 1 gender discrete 2 1 Female 2 Male 2 age continuous 0 3 diagnosis discrete 2 1 TLE 2 extra_TLE Continuous Factors: Mean: StdDev: ------------------- ----- ------- age 30.882 7.631 Number of subjects: 17 Number of factors: 3 (2 discrete, 1 continuous) Number of classes: 4 Number of regressors: 8 ============================================================ Data table loading completed successfully. SUBJECTS_DIR is '/usr/local/freesurfer/subjects' mkdir -p /usr/local/freesurfer/subjects/qdec/stats_tables/ ---------------------------------------------------------- asegstats2table --common-segs --meas volume --tablefile /usr/local/freesurfer/subjects/qdec/stats_tables/aseg.volume.stats.dat --statsfile=aseg.stats --subjects PT1_01 PT1_03 PT1_04 PT1_06 PT1_11 PT1_12 PT1_14 PT1_47 PT1_55 PT1_05 PT1_16 PT1_18 PT1_20 PT1_23 PT1_24 PT1_40 PT1_75 File "/usr/local/freesurfer/bin/asegstats2table", line 195 print 'ERROR: subjects are not specified (use --subjects SUBJECTS)' ^ SyntaxError: invalid syntax I have read some answer in the freesurfer mailing list, but I still don't know how to deal with it. Could you please give me some suggestion? Thanks, Kan

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volume data from part of the brain
by Hang Zeng 19 Aug '19

19 Aug '19

External Email - Use Caution Hi Freesurfers, when I collected the fMRI data, I set the slices to cover part of the brain (only cover the occipital and the temporal lobe). The anatomy scan was of course whole brain. After analysing the data with the pipeline (preproc mkanalysis selxavg3), I overlaid the results on the surf, it looked so weird. So I analysed the data using spm, and used bbregister to register the functional volume to the anatomical data (which also looked weird). The result looked different but doesn't make sense. Because I should see the activations on the occipital and the temporal lobe surf, but instead it appeared on the upper part of the brain surf. I guess this is because of the registration? So how to analyse the data in this situation and how to view the results? Thanks! Zoe

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The R-fMRI Course V3.0 Is Released
by YAN Chao-Gan 18 Aug '19

18 Aug '19

External Email - Use Caution Dear Colleagues, We are pleased to announce the release of The R-fMRI Course V3.0 ( http://rfmri.org/Course) The R-fMRI Course V3.0 is a major update since V2.1. The R-fMRI Course V3.0 systematically introduces the principles of resting-state fMRI (R-fMRI), current research, methodological issues, computational platform and its applications to brain disorders. More importantly, The R-fMRI Course V3.0 explains the data processing details for DPABI/DPABISurf/DPARSF, including data conversion, data preprocessing, temporal dynamic analysis, quality control, statistical analysis and results viewing. A key point of The R-fMRI Course V3.0 is the video course for DPABISurf V1.1. DPABISurf is a surface-based resting-state fMRI data analysis toolbox evolved from DPABI/DPARSF, as easy-to-use as DPABI/DPARSF. DPABISurf is based on fMRIPprep 1.4.1 (Esteban et al., 2018)(RRID:SCR_016216), and based on FreeSurfer 6.0.1 (Dale et al., 1999)(RRID:SCR_001847), ANTs 2.2.0 (Avants et al., 2008)(RRID:SCR_004757), FSL 5.0.9 (Jenkinson et al., 2002)(RRID:SCR_002823), AFNI 20160207 (Cox, 1996)(RRID:SCR_005927), SPM12 (Ashburner, 2012)(RRID:SCR_007037), PALM alpha112 (Winkler et al., 2016), GNU Parallel (Tange, 2011), MATLAB (The MathWorks Inc., Natick, MA, US) (RRID:SCR_001622), Docker (https://docker.com) (RRID:SCR_016445), and DPABI V4.1 (Yan et al., 2016)(RRID:SCR_010501). DPABISurf provides user-friendly graphical user interface (GUI) for pipeline surface-based preprocessing, statistical analyses and results viewing, while requires no programming/scripting skills from the users. DPABISurf is designed to make surface-based data analysis require minimum manual operations and almost no programming/scripting experience. We anticipate The R-fMRI Course V3.0 will guide users to be skilled at how to use this open-source toolbox. The R-fMRI Course V3.0 English Version (http://rfmri.org/Course) (Mostly recorded at The R-fMRI Workshop, July 30~31, 2019) 1. Resting-State fMRI: Current Research, Methodological Issues and Computational Platform 2. Resting-State fMRI: Applications to Brain Disorders 3. The REST-meta-MDD Project: towards a Neuroimaging Biomarker of Major Depressive Disorder 4. Data Processing of Resting-State fMRI: DPARSF 5. The R-fMRI Maps Project 6. Surface-Based Brain Imaging Analysis and DPABISurf 7. DPABI Animal Data Processing 8. Temporal Dynamic Analysis 9. DPABI: Quality Control, Statistical Analysis and Results Viewing 10. DPABISurf: A Surface-Based Resting-State fMRI Data Analysis Toolbox 11. Output structure of DPARSF 12. Output structure of DPABISurf 13. Verification of Reproducibility of R-fMRI Metrics and Reproducible Network Underpinnings of Rumination 14. DPABI: Utilities 15. DPABISurf Advanced: More about FreeSurfer The R-fMRI Course was firstly released on July 15, 2009. During the past 10 years, the course was kept updating, and received 291,425 views. We hope this major update will further help advancing R-fMRI methodology and its application to clinical translational studies. Best, Chao-Gan -- Chao-Gan YAN, Ph.D. Professor, Principal Investigator Director, International Big-Data Center for Depression Research Deputy Director, Magnetic Resonance Imaging Research Center Institute of Psychology, Chinese Academy of Sciences 16 Lincui Road, Chaoyang District, Beijing 100101, China - Initiator <http://rfmri.org/DPARSF>DPABI <http://rfmri.org/DPABI> <http://rfmri.org/DPARSF>, <http://dpabi.org>DPARSF <http://rfmri.org/DPARSF>, PRN <http://rfmri.org/PRN> and The R-fMRI Network <http://rfmri.org> (RFMRI.ORG <http://rfmri.org/>) http://rfmri.org/yan http://scholar.google.com/citations?user=lJQ9B58AAAAJ

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