Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30099 discussions

long_mris_slopes bug
by Katherine Reiter 28 May '14

28 May '14

Hi Freesurfer experts, I'm working on analyzing longitudinal data using the longitudinal 2-stage model. When running the data through long_mris_slopes, I was getting the following error message: ERROR 1 : mris_calc compute sym. pct. change (spc) problem? I saw in previous messages that this is the result of a bug. I found the fix under the release notes, though after downloading it and placing the fix in the bin and makign these files executable, I keep receiving the following error messages. Does anyone have any insight into the problem and possible solutions? mri_convert --frame 0 ./tmp-0001_base_lh_thickness_3f8Byr/glm/beta.mgh ./tmp-0001_base_lh_thickness_3f8Byr/beta0.mgh Traceback (most recent call last): File "/Applications/freesurfer//bin/long_mris_slopes", line 744, in <module> run_cmd(cmd,'mri_convert split frames 0 did not work?') File "/Applications/freesurfer//bin/long_mris_slopes", line 422, in run_cmd retcode = subprocess.call(args) File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 486, in call return Popen(*popenargs, **kwargs).wait() File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 672, in __init__ errread, errwrite) File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 1202, in _execute_child raise child_exception OSError: [Errno 8] Exec format error Thank you, Katherine Reiter, M.S. Clinical Psychology Doctoral Student Marquette University Phone: (414) 288-3807 Email: katherine.reiter(a)marquette.edu

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Corpus Callosum segmentation
by Alessia Giuliano 28 May '14

28 May '14

Dear FreeSurfer team, I'm intrested in the segmentation of Corpus Callosum and in the volumes of its subregions. Freesurfer divides the Corpus Callosum in 5 subregions but I have noticed an inconsistency in the boundary that separates the anterior part from the middle anterior one. In particular, the Rostrum is sometimes included in the anterior part, but other times it is included in the middle anterior part, as you can see comparing the two screenshots that I've attached. How much can I consider this parcellation to be reliable? Thank you, Alessia Giuliano

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Registration of Functional Data to the Inflated Brain
by Sherryse Corrow 27 May '14

27 May '14

Hi FreeSurfer Team, Please help out a FreeSurfer newbie! We are having an issue with mapping our functional data onto the inflated brain. When we finish the mapping, it seems that much of the data is showing up in white-matter space, and therefore, cannot be seen on the external surface of the brain. We later discovered that we were likely using the wrong registration matrix. However, it doesn’t seem like the one we are supposed to use is being produced during recon-all. I am new to FreeSurfer and would greatly appreciate some assistance! To provide you with more detail. Problem: When we run the command line below, and then open the folder experiment.feat/reg/freesurfer, there is no anat2exf.register.dat file. However, there is a file called: anat2exf.register.dat.init. Command Line: Reg-feat2anat -feat OurFeatDirectory.feat -subject P143 Terminal Output: There is no terminal output. No error of any kind. Log File: Attached. Thanks, Sherryse P.S. We submitted this issue previously but were not getting a response, so we tried again in case our thread wasn’t working properly. -- Sherryse Corrow, Ph.D. / Postdoctoral Fellow Human Vision and Eye Movement Lab Department of Ophthalmology & Visual Sciences UBC/VGH Eye Care Centre 360A-2550 Willow Street Vancouver, BC, V5Z 3N9 Tel: 604-875-4111 ext 67672 Cell: 604-315-6717 sherryse.corrow(a)eyecarecentre.org<mailto:sherryse.corrow@eyecarecentre.org>

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Error: no dicom files found
by Caroline Lewis 27 May '14

27 May '14

Hi, I am trying to use the unpacksdcmdir command to convert my dicom files to mgz/nifti, and when i run the command: unpacksdcmdir -src DTI -targ DTI -scanonly DTI/scan.info I get an error message saying there are no dicom files found in the folder, whereas all of the dicom files for that sequence are in that folder (and when I use ls, all of the dcm files are listed). Can anyone help me as to why I am getting this error? Thanks, Caroline

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bbregister and FLAIR
by Kayle Sawyer 27 May '14

27 May '14

Hello, We have been examining the pial surface adjustment with FLAIR scans, and the improvement is quite dramatic. There are MANY areas where the pial surface was clearly wrong and has been substantially improved, considerably reducing (often eliminating) the need for manual pial corrections. I suggest everyone who uses FreeSurfer surfaces acquire a FLAIR scan if they can (see attached for the sequence we’re using). However, for most of our participants, we have run into a serious problem with bbregister. We're running recon-all with two input volumes: -i MEMPRAGE_scan -FLAIR FLAIR_scan Recon-all completes successfully, however the results do not look good due to a bad 'bbregister' registration step. The MEMPRAGE and FLAIR runs were acquired within the same scanning session and they're very well registered to begin with. However, the 'bbregister' step seems to not work well, and they end up grossly misaligned. Here is an example (on the Martinos network): [kslays@ficus ~]$ source /usr/local/freesurfer/nmr-stable53-env; setenv SUBJECTS_DIR /autofs/space/ficus_004/users/SLOTS_subjects; cd $SUBJECTS_DIR; recon-all -all -subjid SLOTS007 \ -i $SUBJECTS_DIR/SLOTS007/3danat/006/MEMPRAGE_RMS.mgz \ -FLAIR $SUBJECTS_DIR/SLOTS007/flair/007/flair.mgz \ -FLAIRpial -mprage -3T -pctsurfcon -qcache -hippo-subfields Check input volume registration (looks good): tkregister2 --targ SLOTS007/mri/orig/001.mgz \ --mov SLOTS007/mri/orig/FLAIRraw.mgz \ --reg NULL --regheader Check bbregister output (looks bad): tkregister2 --mov SLOTS007/mri/orig/FLAIRraw.mgz \ --reg SLOTS007/mri/transforms/FLAIRraw.dat --surf How do we correct the bbregister step? Thanks in advance for your input. -Kayle P.S. If you would like to see other examples, feel free to look at other recons in the same directory. Here is an example where bbregister worked, and the pial corrections are dramatic: freeview -v SLOTS005/mri/FLAIR.mgz \ -f SLOTS005/surf/lh.white:edgecolor=yellow \ SLOTS005/surf/rh.white:edgecolor=yellow \ SLOTS005/surf/lh.pial:edgecolor=red \ SLOTS005/surf/rh.pial:edgecolor=red \ SLOTS005/surf/lh.woFLAIR.pial:edgecolor=green \ SLOTS005/surf/rh.woFLAIR.pial:edgecolor=green \ -ras -37 -46 -42 Kayle Sawyer, PhD Athinoula A. Martinos Center for Biomedical Imaging MGH East Campus, Charlestown Navy Yard Building 149, South Central 1113 - Seat F 149 13th Street Boston, MA 02129 OFFICE:(617) 726-8791 Laboratory of Neuropsychology Boston University School of Medicine L-815 72 E. Concord St Boston, MA 02118 OFFICE:(617) 638-4803 VA Boston Healthcare System Jamaica Plain 150 South Huntington Ave 151-A, D11-126 Boston, MA 02130 OFFICE:(857) 364-4003 FAX: (857) 364-5829

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R: Re: R: Re: R: Re: Problem of size
by Andrea Tateo 27 May '14

27 May '14

Hi FreeSurfer expert, after that I have used the command "recon-all" I would like to obtain wm-lh and wm-rh information ( for example wm-lh-bankssts,wm-lh-caudalanteriorcingulate,wm-lh-caudalmiddlefrontal, ...). I have read that mri_aparc2aseg command can help me, but when I use it I have two problems: 1) When I use the command mri_aparc2aseg --s subject I obtain as output the image "aparc+aseg.mgz" which contains information only about cortical label. 2) When I use the command mri_aparc2aseg --s subject --a.2005 I get the following message: ERROR: Option --a2005 unknown Can you help me? Moreover, the recon-all output in directory /mri is: aparc.a2009s+aseg.mgz, aparc+aseg.mgz, aseg.auto.mgz, aseg.auto_noCCseg.label_intensities.txt , aseg.auto_noCCseg.mgz aseg.mgz, brain.finalsurfs.mgz, brainmask.auto.mgz, brainmask.mgz, brain.mgz, ctrl_pts.mgz, filled.mgz, lh.ribbon.mgz, mri_nu_correct.mni.log, norm.mgz, nu.mgz, nu_noneck.mgz, orig, orig.mgz, rawavg.mgz, rh.ribbon.mgz, ribbon.mgz, segment.dat , T1.mgz, talairach.label_intensities.txt , talairach.log, talairach_with_skull.log, transforms, wm.asegedit.mgz, wm.mgz, wmparc.mgz , wm.seg.mgz Do you think that the searched information is here? Thanks for your help. Best regards, Andrea

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unpacking error
by Caroline Lewis 27 May '14

27 May '14

Hi, I am trying to unpack dicom files and convert them to nifti, but am running into an error. I ran the following command with no issue: unpacksdcmdir -src dicomdir -targ targetdir -scanonly targetdir/scan.info however, when I try to run the next command to actually unpack the data: unpacksdcmdir -src 0008 -targ NIFTI -fsfast \ ? -run 7 3danat mgz 001.mgz \<<NIFTI>> I get the following error message: Missing name for redirect. Thanks, Caroline

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"average" brain files
by Borzello, Mia 27 May '14

27 May '14

Hi Freesurfers, I was wondering if the SurferOutput files for the average subject's brain were somewhere tobe downloaded on the wiki or within the toolbox? Thanks, m

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How to obtain stats on custom anatomical ROI in freeview/freesurfer
by Lucette Cysique 27 May '14

27 May '14

Dear Ruopeng and colleagues, I am interested in following same tracing protocol for the amygdala as in "Neuroimage. 2012 April 2; 60(2): 1226–1235: "A reliable protocol for the manual segmentation of the human amygdala and its subregions using ultra-high resolution MRI” I would like as they did use freeview because it has some versatility and resolution that other programs do not have. I have however one issue Once I have created my ROI in freeview it ends up being by default a .label file. I create my ROI using ROIs and edit ROI tools and simply save it. I have tried to use “mri_label2vol” to get my ROI file (e.g., right_amygdala.label) into a volume file from which I thought I could then compute stats using “mri_segstats” But it does not work, as it seems that the initial .label file does not have the current format? Or required info? My command line output that it cannot read my .label file Thanks for your assistance Lucette

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High Intensity Spots and Surfacing Issues
by Jonathan Holt 27 May '14

27 May '14

Hi all, this is a recurring issue that I'm hoping I can find a solution to. Pictured is a brain with a particularly high intensity area that seems to defy surfacing. Is there a way to work around this? See attached image

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