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30132 discussions

QA tools outliers, use of -gen-asegLUT
by charles laidi 18 Jan '13

18 Jan '13

Dear freesurfers, After reading the documentation on freesurfer web site and searching in the mail archive I wasn't able to find an answer to my question. I'm trying to perform cerebellar segmentation on 100 subjects. The recon-all step went well : every t1 image finished "without error" when I checked the recon-all log. I checked the segmentation result with tmedit and tksurfer (following the recommendation of freesurfer website). I wasn't able to find any problem. After that I use the QA tool. Again, after looking at the snapshots the result appeared correct to me. But for each t1 image, there were between 36 and 45 outliers. So I used the -gen-asegLUT option as suggested in the mail archive (Please find the result below for a t1 image called as100351_conv), but wasn't able to understand the result. The questions I would like to ask you are : 1)What should I do to correct the outliers ? 2) I don't understand this message : "ERROR: Actual file order disagrees with common file order for subject as100351_conv" and this command doesn't work "recon-all -make all -subjid as100351_conv" 3) I don't understand this message : "checking subcortical label: Left-Cerebellum-White-Matter, . +/- . as100351_conv Left-Cerebellum-White-Matter value 1.209679200 is an outlier (avg = . +/- .)..." The value that appears to be an outliers doesn't match with the value that I found in Asegstats for Left-Cerebellum-White-Matter. Thanks a lot for your help, have a nice weekend. Charles Laidi. (medcharleslaidi (a t) gmail.com) ----- Running recon_checker on: mercredi 16 janvier 2013, 22:47:04 (UTC+0100) ----- Most recent FreeSurfer version used to process this subject: /i2bm/local/freesurfer/bin/recon-all ----- All FreeSurfer versions used to process this subject: /i2bm/local/freesurfer/bin/recon-all ----- Checking all output files exist... Running command: /home/charles/Bureau/QAtools_v1.1/recon_all_output_file_checker -subjid as100351_conv -slog /home/charles/Bureau/group_complique//as100351_conv/scripts/recon_checker.log -sumlog /home/charles/Bureau/group_complique//QA/recon_checker.ALL.summary.log -outputfileorderfile /home/charles/Bureau/QAtools_v1.1/default_FOF_FSv5.1 mri/rawavg.mgz last modified 2012-12-14 05:50:00.000000000 +0100 mri/orig.mgz last modified 2012-12-14 05:50:06.000000000 +0100 ERROR: Actual file order disagrees with common file order for subject as100351_conv At least one step in the recon-all stream has been skipped or rerun out of order. Run the following command to rerun any steps which were skipped or for which the output has been modified. recon-all -make all -subjid as100351_conv Alternatively, examine the ReconAllTable for your version of FreeSurfer to identify the recon-all step where the discrepancy is occuring and rerun every recon-all step from that point forward. This subject may have been processed with a different version of FreeSurfer other than the version used to create the common file order file (based on v5.1 by default if not specified by the user). Consider generating an output file order file for your specific dataset using the 'genoutputorderfile' flag. See the '-help' flag for details. actual order ====> common order: .......... ====> ......... mri/rawavg.mgz ====> mri/rawavg.mgz mri/orig.mgz ====> mri/orig.mgz mri/transforms/talairach.xfm ====> mri/transforms/talairach.auto.xfm mri/transforms/talairach.auto.xfm ====> mri/transforms/talairach.xfm mri/nu.mgz ====> mri/nu.mgz mri/T1.mgz ====> mri/T1.mgz mri/brainmask.mgz ====> mri/brainmask.auto.mgz .......... ====> ......... ----- Checking status log output... Running command: /home/charles/Bureau/QAtools_v1.1/recon_all_status_log_checker -subjid as100351_conv -details -slog /home/charles/Bureau/group_complique//as100351_conv/scripts/recon_checker.log -sumlog /home/charles/Bureau/group_complique//QA/recon_checker.ALL.summary.log Using status log: /home/charles/Bureau/QAtools_v1.1/default_status_log_FSv5.1.log as100351_conv COMPLETE ----- Checking asegs for outliers... Using asegLUT: test4 Running command: /home/charles/Bureau/QAtools_v1.1/recon_all_aseg_outlier_checker -subjid as100351_conv -LookupMeansFromFile test4 -slog /home/charles/Bureau/group_complique//as100351_conv/scripts/recon_checker.log -sumlog /home/charles/Bureau/group_complique//QA/recon_checker.ALL.summary.log checking subcortical label: Left-Cerebral-Exterior, 0 +/- checking subcortical label: Left-Cerebral-White-Matter, . +/- . checking subcortical label: Left-Cerebral-Cortex, . +/- . checking subcortical label: Left-Lateral-Ventricle, . +/- . as100351_conv Left-Lateral-Ventricle value .541890500 is an outlier (avg = . +/- .)... checking subcortical label: Left-Inf-Lat-Vent, . +/- . as100351_conv Left-Inf-Lat-Vent value .025678500 is an outlier (avg = . +/- .)... checking subcortical label: Left-Cerebellum-Exterior, . +/- . checking subcortical label: Left-Cerebellum-White-Matter, . +/- . as100351_conv Left-Cerebellum-White-Matter value 1.209679200 is an outlier (avg = . +/- .)... checking subcortical label: Left-Cerebellum-Cortex, . +/- . as100351_conv Left-Cerebellum-Cortex value 3.768655500 is an outlier (avg = . +/- .)... checking subcortical label: Left-Thalamus, . +/- . checking subcortical label: Left-Thalamus-Proper, . +/- . as100351_conv Left-Thalamus-Proper value .490973600 is an outlier (avg = . +/- .)... checking subcortical label: Left-Caudate, 0 +/- checking subcortical label: Left-Putamen, . +/- . as100351_conv Left-Putamen value .490533400 is an outlier (avg = . +/- .)... checking subcortical label: Left-Pallidum, . +/- . as100351_conv Left-Pallidum value .141965600 is an outlier (avg = . +/- .)... checking subcortical label: 3rd-Ventricle, . +/- . as100351_conv 3rd-Ventricle value .083565200 is an outlier (avg = . +/- .)... checking subcortical label: 4th-Ventricle, . +/- . as100351_conv 4th-Ventricle value .152163600 is an outlier (avg = . +/- .)... checking subcortical label: Brain-Stem, . +/- . as100351_conv Brain-Stem value 1.515180400 is an outlier (avg = . +/- .)... checking subcortical label: Left-Hippocampus, . +/- . as100351_conv Left-Hippocampus value .329418900 is an outlier (avg = . +/- .)... checking subcortical label: Left-Amygdala, . +/- . as100351_conv Left-Amygdala value .146147500 is an outlier (avg = . +/- .)... checking subcortical label: Left-Insula, . +/- . checking subcortical label: Left-Operculum, . +/- . checking subcortical label: Line-1, . +/- . checking subcortical label: Line-2, . +/- . checking subcortical label: Line-3, . +/- . checking subcortical label: CSF, . +/- . as100351_conv CSF value .103080900 is an outlier (avg = . +/- .)... checking subcortical label: Left-Lesion, . +/- . checking subcortical label: Left-Accumbens-area, . +/- . as100351_conv Left-Accumbens-area value .060014400 is an outlier (avg = . +/- .)... checking subcortical label: Left-Substancia-Nigra, . +/- . checking subcortical label: Left-VentralDC, . +/- . as100351_conv Left-VentralDC value .304840900 is an outlier (avg = . +/- .)... checking subcortical label: Left-undetermined, . +/- . checking subcortical label: Left-vessel, . +/- . as100351_conv Left-vessel value .008143700 is an outlier (avg = . +/- .)... checking subcortical label: Left-choroid-plexus, . +/- . as100351_conv Left-choroid-plexus value .140791700 is an outlier (avg = . +/- .)... checking subcortical label: Left-F3orb, . +/- . checking subcortical label: Left-lOg, . +/- . checking subcortical label: Left-aOg, . +/- . checking subcortical label: Left-mOg, . +/- . checking subcortical label: Left-pOg, . +/- . checking subcortical label: Left-Stellate, . +/- . checking subcortical label: Left-Porg, . +/- . checking subcortical label: Left-Aorg, . +/- . checking subcortical label: Right-Cerebral-Exterior, . +/- . checking subcortical label: Right-Cerebral-White-Matter, . +/- . checking subcortical label: Right-Cerebral-Cortex, . +/- . checking subcortical label: Right-Lateral-Ventricle, . +/- . as100351_conv Right-Lateral-Ventricle value .284664900 is an outlier (avg = . +/- .)... checking subcortical label: Right-Inf-Lat-Vent, . +/- . as100351_conv Right-Inf-Lat-Vent value .009904500 is an outlier (avg = . +/- .)... checking subcortical label: Right-Cerebellum-Exterior, . +/- . checking subcortical label: Right-Cerebellum-White-Matter, . +/- . as100351_conv Right-Cerebellum-White-Matter value 1.212467100 is an outlier (avg = . +/- .)... checking subcortical label: Right-Cerebellum-Cortex, . +/- . as100351_conv Right-Cerebellum-Cortex value 3.943269600 is an outlier (avg = . +/- .)... checking subcortical label: Right-Thalamus, . +/- . checking subcortical label: Right-Thalamus-Proper, . +/- . as100351_conv Right-Thalamus-Proper value .520393900 is an outlier (avg = . +/- .)... checking subcortical label: Right-Caudate, 0 +/- checking subcortical label: Right-Putamen, . +/- . as100351_conv Right-Putamen value .503959600 is an outlier (avg = . +/- .)... checking subcortical label: Right-Pallidum, . +/- . as100351_conv Right-Pallidum value .119368500 is an outlier (avg = . +/- .)... checking subcortical label: Right-Hippocampus, . +/- . as100351_conv Right-Hippocampus value .360013100 is an outlier (avg = . +/- .)... checking subcortical label: Right-Amygdala, . +/- . as100351_conv Right-Amygdala value .143212800 is an outlier (avg = . +/- .)... checking subcortical label: Right-Insula, . +/- . checking subcortical label: Right-Operculum, . +/- . checking subcortical label: Right-Lesion, . +/- . checking subcortical label: Right-Accumbens-area, . +/- . as100351_conv Right-Accumbens-area value .065150100 is an outlier (avg = . +/- .)... checking subcortical label: Right-Substancia-Nigra, . +/- . checking subcortical label: Right-VentralDC, . +/- . as100351_conv Right-VentralDC value .298237800 is an outlier (avg = . +/- .)... checking subcortical label: Right-undetermined, . +/- . checking subcortical label: Right-vessel, . +/- . as100351_conv Right-vessel value .005575900 is an outlier (avg = . +/- .)... checking subcortical label: Right-choroid-plexus, . +/- . as100351_conv Right-choroid-plexus value .143066100 is an outlier (avg = . +/- .)... checking subcortical label: Right-F3orb, . +/- . checking subcortical label: Right-lOg, . +/- . checking subcortical label: Right-aOg, . +/- . checking subcortical label: Right-mOg, . +/- . checking subcortical label: Right-pOg, . +/- . checking subcortical label: Right-Stellate, . +/- . checking subcortical label: Right-Porg, . +/- . checking subcortical label: Right-Aorg, . +/- . checking subcortical label: 5th-Ventricle, . +/- . as100351_conv 5th-Ventricle value .000293400 is an outlier (avg = . +/- .)... checking subcortical label: Left-Interior, . +/- . checking subcortical label: Right-Interior, . +/- . checking subcortical label: Left-Lateral-Ventricles, . +/- . checking subcortical label: Right-Lateral-Ventricles, . +/- . checking subcortical label: WM-hypointensities, . +/- . as100351_conv WM-hypointensities value .098165300 is an outlier (avg = . +/- .)... checking subcortical label: Left-WM-hypointensities, . +/- . checking subcortical label: Right-WM-hypointensities, . +/- . checking subcortical label: non-WM-hypointensities, . +/- . as100351_conv non-WM-hypointensities value .001393900 is an outlier (avg = . +/- .)... checking subcortical label: Left-non-WM-hypointensities, . +/- . checking subcortical label: Right-non-WM-hypointensities, . +/- . checking subcortical label: Left-F1, . +/- . checking subcortical label: Right-F1, . +/- . checking subcortical label: Optic-Chiasm, . +/- . as100351_conv Optic-Chiasm value .018635200 is an outlier (avg = . +/- .)... checking subcortical label: Corpus_Callosum, . +/- . checking subcortical label: Left-Amygdala-Anterior, . +/- . checking subcortical label: Right-Amygdala-Anterior, . +/- . checking subcortical label: Dura, . +/- . checking subcortical label: Left-wm-intensity-abnormality, . +/- . checking subcortical label: Left-caudate-intensity-abnormality, . +/- . checking subcortical label: Left-putamen-intensity-abnormality, . +/- . checking subcortical label: Left-accumbens-intensity-abnormality, . +/- . checking subcortical label: Left-pallidum-intensity-abnormality, . +/- . checking subcortical label: Left-amygdala-intensity-abnormality, . +/- . checking subcortical label: Left-hippocampus-intensity-abnormality, . +/- . checking subcortical label: Left-thalamus-intensity-abnormality, . +/- . checking subcortical label: Left-VDC-intensity-abnormality, . +/- . checking subcortical label: Right-wm-intensity-abnormality, . +/- . checking subcortical label: Right-caudate-intensity-abnormality, . +/- . checking subcortical label: Right-putamen-intensity-abnormality, . +/- . checking subcortical label: Right-accumbens-intensity-abnormality, . +/- . checking subcortical label: Right-pallidum-intensity-abnormality, . +/- . checking subcortical label: Right-amygdala-intensity-abnormality, . +/- . checking subcortical label: Right-hippocampus-intensity-abnormality, . +/- . checking subcortical label: Right-thalamus-intensity-abnormality, . +/- . checking subcortical label: Right-VDC-intensity-abnormality, . +/- . checking subcortical label: Epidermis, . +/- . checking subcortical label: Conn-Tissue, . +/- . checking subcortical label: SC-Fat/Muscle, . +/- . checking subcortical label: CSF-SA, . +/- . checking subcortical label: Muscle, . +/- . checking subcortical label: Ear, . +/- . checking subcortical label: Adipose, . +/- . checking subcortical label: Spinal-Cord, . +/- . checking subcortical label: Soft-Tissue, . +/- . checking subcortical label: Nerve, . +/- . checking subcortical label: Bone, . +/- . checking subcortical label: Air, . +/- . checking subcortical label: Orbital-Fat, . +/- . checking subcortical label: Tongue, . +/- . checking subcortical label: Nasal-Structures, . +/- . checking subcortical label: Globe, . +/- . checking subcortical label: Teeth, . +/- . checking subcortical label: Left-Caudate/Putamen, . +/- . checking subcortical label: Right-Caudate/Putamen, . +/- . checking subcortical label: Left-Claustrum, . +/- . checking subcortical label: Right-Claustrum, . +/- . checking subcortical label: Cornea, . +/- . checking subcortical label: Diploe, . +/- . checking subcortical label: Vitreous-Humor, . +/- . checking subcortical label: Lens, . +/- . checking subcortical label: Aqueous-Humor, . +/- . checking subcortical label: Outer-Table, . +/- . checking subcortical label: Inner-Table, . +/- . checking subcortical label: Periosteum, . +/- . checking subcortical label: Endosteum, . +/- . as100351_conv has 34 outliers ... ----- Checking white matter SNR measurements... SNR: Anatomical signal-to-noise ratio in white matter mWM: Mean white matter intensity value stdWM: Standard deviation of white matter intensity value voxWM: Total number of white matter voxels in eroded mask Running command: /home/charles/Bureau/QAtools_v1.1/recon_all_wm-anat-snr_checker -subjid as100351_conv -slog /home/charles/Bureau/group_complique//as100351_conv/scripts/recon_checker.log -sumlog /home/charles/Bureau/group_complique//QA/recon_checker.ALL.summary.log wm-anat-snr results (as100351_conv): SNR meanWM stdWM voxWM 21,16 108,11 5,11 44847 -----

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Re: [Freesurfer] nu_correct problem
by Gregory Kirk 18 Jan '13

18 Jan '13

Petr why do you keep trying to name your input files something.mgz, when you were in wisconsin i told you the inputs always need to be 001.mgz at this point i think you need to get invited to upload one of your data sets to ugh and see if there is a problem with the data or is it a problem with your computer. Can someone there at martinos invite Petr to upload the dataset and tell him the mechanism for doing this ? On 01/18/13, zach.petr(a)post.cz wrote: > > > > > I tried on another standar PC (4 core processor) with XP Win recon-all in VirtualBox (latest edition) running Ubuntu. > > > > I attach file folder with patient brain - first in VirtualBox as described and then in command line of terminal Ubuntu window: > > sudo mount - vboxsf folder /home/virtualuser/freesurfer/subjects/folder > > > > Then I convert original TrioTim scanner files using mri_convert -it IMA -ot mgz filename foldername.mgz > > * here is slight problem - recon log shows that mri_convert recognizes itself that although my brain files are labeled as IMA that they are not old Siemens files, so that it unpacks them as DICOM and suggests that if it fails I should run mri_convert as DICOM > > But after all mri_convert succesfully writes foldername.mgz file as a result of conversion in foldername directory > > > > Ok, then I run recon-all -subjid foldername -autorecon1 -cw256 > > Now -cw256 was suggested in another error run because files do not fit in 256 matrix > > Recon stops and sayz no 001.mgz files in /mri/orig directory > > So I copy converted foldername.mgz from foldername directory into /mri/orig directory and rename it to 001.mgz > > *now here is my question: do all people get 001.mgz file the same way as me? > > Then when I run recon-all -subjid foldername -autorecon1 -cw256 it halts with error at nu_correct as you can see in attached recon-all.log file > > > > Petr

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pial not computing
by Borzello, Mia 18 Jan '13

18 Jan '13

Hi Freesurfers, I just ran a recon, and it seems that only the lh.pial computed, but not the rh.pial. What would be the cause of this? Thanks, m

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commands to extract thickness values
by Catherine Bois 18 Jan '13

18 Jan '13

Hi, I am trying to extract stats files from my subjects using this command aparcstats2table --hemi lh --subjects EHRS_* --skip --meas thickness --parc --aparc --tablefile lh.thick.table however I keep getting this error message Parsing the .stats files Skipping /sdata/images/projects/EHRS/2/Freesurfer_EHRS/READYFORANALYSIS/EHRS_0970_3/stats/lh.--aparc.stats Building the table.. Traceback (most recent call last): File "/usr/local2/freesurfer/bin/aparcstats2table", line 338, in ? rows, columns, table = sanitize_table(options, pretable) File "/usr/local2/freesurfer/bin/aparcstats2table", line 253, in sanitize_table _spec, _parc_measure_map = dt[0] IndexError: list index out of range [cbois@poplar ~]$ I have previously used this command on version 5, I now have version 5.1, have the commands possibly changed? Thanks, Cathy -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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v5.2.0 beta, round two
by Nick Schmansky 18 Jan '13

18 Jan '13

For those willing and brave enough, another beta of v5.2.0 has been posted here for you to download and test: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.2.0-BETA/ The Mac builds should work (note: the lion build is 64b, snow-leopard is 32b). The final release still awaits some critical improvements to the Tracula stream, but the main recon-all stream with this beta is final. The final release is expected the first week of February. Freesurfer team

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longitudinal analysis
by paul horton 18 Jan '13

18 Jan '13

Hi guys, I am currently running a longitudinal analysis on a set of scan. It is currently running and so far it has taken 5 days. It seems to be taking a large amount of time on a process called labelling slice. I have run the same analysis on other subjects which took about 6 hours to complete. So I was wondering if you know of any reason why a set of scans would take longer to process than others. I have checked the inital scans and nothing seems obviously wrong with them. Best Wishes Paul

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nu_correct problem
by zach.petr＠post.cz 18 Jan '13

18 Jan '13

I tried on another standar PC (4 core processor) with XP Win recon-all in VirtualBox (latest edition) running Ubuntu. I attach file folder with patient brain - first in VirtualBox as described and then in command line of terminal Ubuntu window: sudo mount - vboxsf folder /home/virtualuser/freesurfer/subjects/folder Then I convert original TrioTim scanner files using mri_convert -it IMA -ot mgz filename foldername.mgz * here is slight problem - recon log shows that mri_convert recognizes itself that although my brain files are labeled as IMA that they are not old Siemens files, so that it unpacks them as DICOM and suggests that if it fails I should run mri_convert as DICOM But after all mri_convert succesfully writes foldername.mgz file as a result of conversion in foldername directory Ok, then I run recon-all -subjid foldername -autorecon1 -cw256 Now -cw256 was suggested in another error run because files do not fit in 256 matrix Recon stops and sayz no 001.mgz files in /mri/orig directory So I copy converted foldername.mgz from foldername directory into /mri/orig directory and rename it to 001.mgz *now here is my question: do all people get 001.mgz file the same way as me? Then when I run recon-all -subjid foldername -autorecon1 -cw256 it halts with error at nu_correct as you can see in attached recon-all.log file Petr

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Freesurfer vertex wise area reference
by MAHINDA YOGARAJAH 17 Jan '13

17 Jan '13

Hi, Sorry to be a little more specific - I am aware of freesurfer area references such as the WInkler reference but basically wanted a few lines, and the most appropriate references, that summarises the technical approach used for group area comparisons in qdec (using updated mris_preproc), and simple ROI group area comparisons. Thanks, Mahinda

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Merging .annot files
by Chris McNorgan 17 Jan '13

17 Jan '13

Hello all, I posted this question on the cmtk users google group, but no takers, and perhaps this is the more appropriate venue anyways. I've been successfully using cmtk within iPython. After running connectomemapper parcellate() to get the Lausanne parcellation scheme, I get six .annot files: ?h.myaparcP1_16.annot, ?h.myaparcP17_28.annot, and ?h.myaparcP29_66.annot, for each of lh and rh. Each of these .annot files label the entire cortical surface, but each of the 36 major anatomical regions (e.g., posteriorcingulate) for each hemisphere are further subdivided in only one of the three .annot files; the other two files use the original definition of the major region. In other words, in order to use these .annot files to work with the Lausanne sub-parcellations for the entire cortical surface, one has to run the same procedure using each of the 3 .annot files, and then figure out which .annot file provided the desired information. I was wondering whether it is possible to merge the three annot files to create a single .annot file for each hemisphere in which ALL of the 36 major anatomical regions have been subdivided, rather than three files containing parcellations of different subsets of these regions? Though I have been using scripts to sift through multiple sets of results to find what I'm looking for, some manual chores would be easier if I only had to work with a single file. The fact that the same vertices are labeled in all files (but are given the macro-region label in 2 files, and the sub-parcelation label in 1 file) makes me think that it's not a simple matter of concatenating the annotation files. Thanks, Chris

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problem with AutoReco3 mapping
by jonwieser＠netzero.net 17 Jan '13

17 Jan '13

I did an AutoRecon3 on a brain and when i viewed the results. it failed to classify some the tgray and white matter in the left hemisphere. the area misses is on the extreme left side of the brain, within 10 mm of the left side of the hemisphere. are there some arguments i change change to fix this. Jon Wieser jonwieser(a)netzero.com "When the going gets tough, switch to power tools." - Red Green ____________________________________________________________ One Trick to Stay Asleep If you struggle to fall asleep, or stay asleep, try this&#8230 http://thirdpartyoffers.netzero.net/TGL3241/50f85712990b57112b48st01duc

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