Freesurfer

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30099 discussions

Color scale in TkSurfer
by Zeynep Akalin Acar 13 Jun '14

13 Jun '14

I'm plotting potential distributions on a cortical surface using TkSurfer. The color scale "Heat" gives the most comprehensible plots. However, I would like to have the maximum values to be plotted in red instead of yellow, and minimum in dark blue instead of light blue. max +threshold 0 -threshold min -> Overlay values yellow red gray dark blue light blue -> Heat colorscale red yellow gray light blue dark blue -> Desired colorscale Is there a way to have the color scale like this? I tried the color scales 'green red' and 'blue red', however, when I select these scales the brain surface disappears. Thank you, Zeynep.

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FS GUI no glx extension
by Arman Eshaghi 13 Jun '14

13 Jun '14

Hi, On a remote server forwarding X and running Ubuntu 14.04 I am having difficulty running tkregister2, with this error: * No glx extension!* * register: ### tkoInitWindow(name) failed* Also tried * export LIBGL_ALWAYS_INDIRECT=y* which did not work. Any input is highly appreciated. All the best, Arman

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Re: [Freesurfer] brain.finalsurfs.manedit.mgz file edits & longitudinal processing
by Martin Reuter 13 Jun '14

13 Jun '14

Hi Doug, The second command below should copy your edits from the finalsurf manedit in cross to the long directory. You can try that command manually with a fresh volume. If it really does not carry over, can you send me the two volumes (edited one from cross and the unedited one from long) so that I can take a look. Maybe your edits are wrong (deletes are not zero, but adifferent number, I think 1). Not sure what consequences it has to copy to brainmask but I would not recommend it. Martin Sent via my smartphone, please excuse brevity. -------- Original message -------- From: Douglas Merkitch <Douglas_Merkitch(a)rush.edu> Date:06/05/2014 9:51 PM (GMT+01:00) To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] brain.finalsurfs.manedit.mgz file edits & longitudinal processing Hello Martin and FreeSurfer experts, I've checked the recon-all.log from the 2nd tp of one of the longitudinal subject directories (1004_1.long.1004_base) and found the following 4 lines using your search criteria: 1. \n mri_mask -transfer 255 -keep_mask_deletion_edits brainmask.auto.mgz brainmask_1004_base.mgz brainmask.auto.mgz \n 2. \n mri_mask -transfer 255 -keep_mask_deletion_edits -xform /Users/glennstebbins/Desktop/harlow_mount/JenG/ResearchAssistant/data/freesurfer_v5.1/1004_base/mri/transforms/1004_1_to_1004_base.lta brain.finalsurfs.mgz /Users/glennstebbins/Desktop/harlow_mount/JenG/ResearchAssistant/data/freesurfer_v5.1/1004_1/mri/brain.finalsurfs.manedit.mgz brain.finalsurfs.mgz \n 3. \n mri_mask -transfer 255 -keep_mask_deletion_edits -xform /Users/glennstebbins/Desktop/harlow_mount/JenG/ResearchAssistant/data/freesurfer_v5.1/1004_base/mri/transforms/1004_1_to_1004_base.lta wm.mgz /Users/glennstebbins/Desktop/harlow_mount/JenG/ResearchAssistant/data/freesurfer_v5.1/1004_1/mri/wm.mgz wm.mgz \n 4. \n mri_mask -transfer 255 -keep_mask_deletion_edits brain.finalsurfs.mgz brain.finalsurfs.manedit.mgz brain.finalsurfs.mgz \n Does any of this stand out to you? In visually comparing the brain.finalsurfs.manedit.mgz files between the cross and long, the edits do not appear to transfer to the long as has happened previously. However, when the brain.finalsurfs.manedit.mgz file is copied to the brianmask.mgz file (in the base and cross time points), and the longitudinal processes stream is run, the edits now contained in the brainmask.mgz files do seem to transfer. Can you think of any complications (other than cerebellar) that would arise from copying the brain.finalsurfs.manedit.mgz file (where edits were made) to the brainmask.mgz in the cross-sectional and base directories and rerunning the longitudinal processing stream from scratch? Thanks for all your help! Doug Doug Merkitch Neurological Sciences Rush University Medical Center Phone: (312) 563-3853 Fax: (312) 563-4660 Email: Douglas_Merkitch(a)rush.edu On May 19, 2014, at 3:52 PM, Martin Reuter <mreuter(a)nmr.mgh.harvard.edu> wrote: Hi Doug, Usually I edit dura etc in the brainmask and only touch finalsurfs for cerebellum edits. But your way should also work (at least I don't know right now why it should not). Anyway, I looked at recon-all and in the mask BFS step, it does copy the edits over from the cross into the long (if it's working as it should, see line 2565). That command should be printed in your log file of the long run and you can search and double-check that it is there. (mri_mask -transfer 255 -keep_mask_deleting_edits -xform .....) You can also compare the brain_finalsurfs between cross and long in each time point to make sure the edits did get transferred. Be aware that these two images are not registered. The cross is in the original space, the long in the same space as the base and all other time points. So you may have to search around to find the same exact place. Anyway, assuming edits do get through, the finalsurfs is then used in the mris_make_surfaces step. In long, this step is different from cross, as it takes the surfaces from the base as initialization and then fine tunes them. So you also have to check the surfaces in the base are all OK. That is essential as long takes it from there. Best, Martin On 05/16/2014 12:29 PM, Douglas Merkitch wrote: Dear Martin and FreeSurfer experts, Thanks for your response. I have just finished re-running some subjects from scratch in 5.3 and it appears that the edits from brain.finalsurfs.manedit.mgz are not being applied to the longitudinal subject directories. Just to clarify, I have been doing ALL of the pial surface edits in the brain.finalsurfs.manedit.mgz, not just the pial surface edits that have extended into the cerebellum. The rationale for doing this is mainly continuity, as the previous research assistant made all pial surface edits in this way because of a response she had received from the FS forum saying that there shouldn't be any problem with performing all the pial surface edits in the brain.finalsurfs.manedit.mgz file. Is there something in the FreeSurfer longitudinal processing code that would treat edits near the cerebellum of the brain.finalsurfs.manedit.mgz file differently from those made in other parts of the brain (e.g. lateralorbitofrontal, dura, etc.,)? Can you think of anything else that would be causing this or anything that I could try to get the longitudinal processing stream to incorporate the edits from the brain.finalsurfs.manedit.mgz file? Thanks for your help! Doug Merkitch Neurological Sciences Rush University Medical Center Phone: (312) 563-3853 Fax: (312) 563-4660 Email: Douglas_Merkitch(a)rush.edu Begin forwarded message: From: Martin Reuter <mreuter(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] brain.finalsurfs.manedit.mgz file edits & longitudinal processing Date: May 2, 2014 4:20:17 PM CDT To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Hi Doug, so you 1. edited the cross sectionals and surfaces look fine (make sure you edit the brain.finalsurfs.manedit.mgz file, which you create as a copy of the brain.finalsurfs.mgz) 2. checked/edited the base and surfaces look fine too 3. ran the longitudinal from scratch (w/o any edits) and then in the long, the surface looks not good? Edits should automatically be copied from cross->long (if the manedit file exist). Surfaces are taken from the base to initialize longitudinal processing. That is why both step1 and step2 above are important. Step3 is a good idea to make sure that the longs are not polluted by some earlier edits. For example edits from cross are only copied over if the long has no manedit file, else only the edits in the long will be used. (I think this also answers some of the questions in the archive mail 1 you cite below, the archive mail 2 is a question about cross sectional processing, but I think there the problem is that brainmask.finalsurfs.mgz was edited directly, not the manedit file, so edits probably get overwritten). I also have the feeling that we fixed something about the editing in longitudinal processing after 5.1, but cannot find it documented on the wiki (so not sure). You may want to try to run this with 5.3 if it does not work with 5.1 Best, Martin On 05/02/2014 10:45 AM, Douglas Merkitch wrote: Dear Freesurfer experts, I have a question regarding longitudinal edits. Specifically the brain.finalsurfs.manedit.mgz file and the longitudinal processing stream in Freesufer 5.1 on a Mac (freesurfer-i686-apple-darwin9.8.0-stable5-20110525). The problem that I am having is that the edits saved in the brain.finalsurfs.manedit.mgz file do not carry over when processing longitudinally. Previous posts have addressed this topic, but have not (to my knowledge) solved the issue. Please see the threads from the Freesurfer archive below for a brief context: 1. http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg27695.html 2. http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg33471.html Please let me know if more information is needed to understand the issue. Any insight/ideas regarding this issue would be greatly appreciated! Thanks, Doug Doug Merkitch Neurological Sciences Rush University Medical Center Phone: (312) 563-3853 Fax: (312) 563-4660 Email: Douglas_Merkitch(a)rush.edu _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Martin Reuter, Ph.D. Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreuter(a)nmr.mgh.harvard.edu reuter(a)mit.edu Web : http://reuter.mit.edu _______________________________________________ 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 -- Martin Reuter, Ph.D. Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreuter(a)nmr.mgh.harvard.edu reuter(a)mit.edu Web : http://reuter.mit.edu _______________________________________________ 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.

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TRACULA: ERROR in -qa Flag
by Shantanu Ghosh 13 Jun '14

13 Jun '14

Dear Anastasia and Freesurfer experts, I am trying to set up an analysis of motion parameters using the flag -q from a set of DTI Dicoms located on the Martinos cluster, but I am facing problems -- it says "ERROR: flag -qa unrecognized". My .tcshrc is set to Freesurfer5.3 and FSL. What am I doing wrong? My config file is attached and here are my commands. cd /autofs/space/glia_001/users/shantanu/dtistudy/ setenv PATH /usr/pubsw/packages/python/epd/bin:${PATH} setenv FSENV_KEEP_PROMPT setenv MNE_ROOT /usr/pubsw/packages/mne/stable setenv SUBJECTS_DIR /autofs/space/calvin_001/marvin/1/users/MRI/WMA/recons setenv FSL_DIR /usr/pubsw/packages/fsl/5.0.0 source /usr/local/freesurfer/nmr-stable53-env source /usr/pubsw/packages/mne/stable/bin/mne_setup ----My console output----- glia:shantanu[120] mynmr53 -------- freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) WARNING: /autofs/space/calvin_001/marvin/1/users/MRI/WMA/recons does not exist FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 FSFAST_HOME /usr/local/freesurfer/stable5_3_0/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /autofs/space/calvin_001/marvin/1/users/MRI/WMA/recons MNI_DIR /usr/local/freesurfer/stable5_1_0/mni FSL_DIR /usr/pubsw/packages/fsl/5.0.0 MNE software location set to: /usr/pubsw/packages/mne/stable MATLAB software not available /usr/pubsw/packages/mne/stable/bin already in PATH /usr/pubsw/packages/mne/stable/lib added to LD_LIBRARY_PATH /usr/pubsw/packages/mne/stable/share/app-defaults/%N added to XUSERFILESEARCHPATH Note: Remember to set SUBJECTS_DIR and SUBJECT environment variables correctly. Note: FreeSurfer environment is needed to access tkmedit from mne_analyze. glia:shantanu[121] trac-all -qa -s 008801 -c /autofs/space/glia_001/users/shantanu/dtistudy/dticonfigfile.txt ERROR: flag -qa unrecognized -qa -s 008801 -c /autofs/space/glia_001/users/shantanu/dtistudy/dticonfigfile.txt glia:shantanu[122] Thanks in advance for all help. Shantanu -- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging -- Not only is the universe stranger than we think, it is stranger than we can think. -Werner Heisenberg

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Re: [Freesurfer] Computing LGI values for the longitudinal stream
by Martin Reuter 13 Jun '14

13 Jun '14

Hi Tudor, You'd add the lgi only to the third step (the -long runs). And you could do a two stage model with it. Martin Sent via my smartphone, please excuse brevity. -------- Original message -------- From: Tudor Popescu <tudor3(a)gmail.com> Date:06/10/2014 11:51 PM (GMT+01:00) To: free surfer <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Computing LGI values for the longitudinal stream Dear FS list, I did all 3 steps of the longitudinal stream (cross, base, long), plus the long_mris_slopes for my three-group & two-timepoint data set. This gave me files for thickness and area, but I'd also like to do analysis for lGI. To that end, I first did recon-all -s subj -localGI and then recon-all -base subj -tp subj_prescan -tp subj_postscan -localGI These commands ended with the "abberantly high lGI value" error for 3 subjects out of the total of 72, and for those I then ran what I knew was the standard workaround: recon-all -autorecon2-wm -randomness -autorecon3 -hemi ?h -s subj However received the error It appears that this subject ID is an existing base/template from longitudinal processing (-base). Please make sure you pass all necessary flags. I was therefore wondering if it is in fact the case that the longitudinal stream for lGI is done by simply adding -localGI to the normal commands shown in the tutorial (i.e. cross, base, long + the long_mris_slopes command)? Also, assuming the lGI values will be eventually be computed as part of the longitudinal stream, are lGI analyses done in the same way as for thickness, i.e. two-stage model and QDEC? Many thanks for any help. Tudor

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Re: [Freesurfer] Longitudinal design
by Martin Reuter 13 Jun '14

13 Jun '14

Hi Tudor, 1. There is a new version of freeview, I think you can download it somewhere. The tutorial also gives the tk surfer command line, which will work. But the visualization is not necessary. 2.probably the qdec table has errors, eg different line breaks? Can you split it into blocks to see which block it does not load? 3. To look at change you'd look at rate or percent change. Avg is just the average thickness of each subject across time. I never really used qdec, but probably you cannot do three groups. Best Martin Sent via my smartphone, please excuse brevity. -------- Original message -------- From: Tudor Popescu <tudor3(a)gmail.com> Date:06/12/2014 10:00 PM (GMT+01:00) To: free surfer <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Longitudinal design Hi Martin There were in fact some problems with the lGI values, as it wasn't clear at which of the 3 preprocessing steps (cross, base, long) the --pial_lgi flag had to be added. I asked about that in a different email, and meanwhile continued with the analysis for the existing measures (area and thickness). Issues I encountered: 1) After using the tutorial command freeview -f subj/surf/lh.pial:overlay=subj/surf/lh.long.thickness-avg.fwhm15.mgh:overlay_threshold=0,3.5:overlay=subj/surf/lh.long.thickness-stack.mgh:annot=subj/label/lh.aparc.annot:annot_outline=1 --timecourse --colorscale I received errors about the option 'timecourse' and the sub-option flag 'annot_outline' being unrecongised. Is there a more recent version of freeview? I'm using FS 5.3, which I thought was the latest. Either way, I guess that this particular visualisation is not essential to the analysis. 2) When I load my cross.qdec.table.dat (attached) into QDEC, "Number of subjects" in the Subjects tab shows as 67, even though I have 72 subjects, all of which appear correctly entered on each line of the cross.qdec.table.dat ! 3) If I understood correctly, if one wants to see how thickness changed across time points and across the different groups, i.e. test the interaction, then "long.thickness-avg" has to be selected as Measure in QDEC. After doing this, and choosing group as a discrete factor, the mri_glmfit --y command fails with the errors "ERROR: QdecGlmDesign::GenerateContrasts: factor 1 must have 2 levels". I guess this is because I have 3 groups and not 2. The question is, can I somehow do the 3 pairwise comparisons between my 3 groups in QDEC rather than at the command line (mri_glmfit) ? Many thanks! Tudor On 7 June 2014 23:24, Martin Reuter <mreuter(a)nmr.mgh.harvard.edu> wrote: Hi Tudor. For the mri_concat command at the end, does it work when you run it directly? It should not. Are the input files there. Is the dimension correct (you can run mri info on them). Since they are just surface maps, just like thickness, their dimensions should agree (eith each other and with thickness, and number of vertices of surfaces). Best Martin Sent via my smartphone, please excuse brevity. -------- Original message -------- From: Tudor Popescu Date:06/07/2014 9:55 PM (GMT+01:00) To: Freesurfer support list Subject: Re: [Freesurfer] Longitudinal design I should add that the commands for thickness, i.e. long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas thickness --hemi ?h --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time day --qcache fsaverage --sd $SUBJECTS_DIR finished without error, and for some reason, so did the surface area commands, when I ran them a second time. Also, I realised that for lGI, the flag for --meas was pial_lgi and not just lgi. However, the command long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas pial_lgi --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time day --qcache fsaverage --sd $SUBJECTS_DIR resulted in this error, similar for both hemispheres: SUBJECT F02 Stacking Within-Subject Maps mri_concat /vols/Scratch/tpopescu/learning/FS/F02_d1.long.F02/surf/rh.pial_lgi /vols/Scratch/tpopescu/learning/FS/F02_d5.long.F02/surf/rh.pial_lgi --o /vols/Scratch/tpopescu/learning/FS/F02/surf/rh.long.pial_lgi-stack.mgh ERROR 1 : mri_concat stacking did not work? Thanks again for your help! On 6 June 2014 17:45, Tudor Popescu <tudor3(a)gmail.com> wrote: Hi Martin, thanks a lot for your answers. The slopes command is giving me errors though, see below. I also attach the long.qdec.table.dat that I'm using. I should point out that those ?h.long.cortex.label files mentioned in the error messages are in fact at their expected locations, and appear to be fine (i.e. are not size 0) In case anyone else can advice about question 1, I'd be really grateful! Command Error long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas area --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time day --qcache fsaverage --sd $SUBJECTS_DIR No such file or directory mris_label_calc: could not open label file /vols/Scratch/tpopescu/learning/FS/F02/label/lh.long.cortex.label Invalid argument mris_label_calc: mris_label_calc.cpp:127: int main(int, char**): Assertion `l2 != __null' failed. long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas area --hemi rh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time day --qcache fsaverage --sd $SUBJECTS_DIR mris_calc: could not open label file /vols/Scratch/tpopescu/learning/FS/F23/label/rh.long.cortex.label Invalid argument mris_calc: could not read label file /vols/Scratch/tpopescu/learning/FS/F23/label/rh.long.cortex.label Invalid argument long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas lGI --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time day --qcache fsaverage --sd $SUBJECTS_DIR mris_label_calc: mris_label_calc.cpp:127: int main(int, char**): Assertion `l2 != __null' failed. SUBJECT F02 Intersecting Within-Subject Cortex Label cp /vols/Scratch/tpopescu/learning/FS/F02_d1.long.F02/label/lh.cortex.label /vols/Scratch/tpopescu/learning/FS/F02/label/lh.long.cortex.label mris_label_calc intersect /vols/Scratch/tpopescu/learning/FS/F02_d5.long.F02/label/lh.cortex.label /vols/Scratch/tpopescu/learning/FS/F02/label/lh.long.cortex.label /vols/Scratch/tpopescu/learning/FS/F02/label/lh.long.cortex.label ERROR -6 : mris_label_calc intersect did not work? long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas lGI --hemi rh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time day --qcache fsaverage --sd $SUBJECTS_DIR No such file or directory mris_label_calc: could not open label file /vols/Scratch/tpopescu/learning/FS/F02/label/rh.long.cortex.label Invalid argument mris_label_calc: mris_label_calc.cpp:127: int main(int, char**): Assertion `l2 != __null' failed. On 5 June 2014 16:00, Martin Reuter <mreuter(a)nmr.mgh.harvard.edu> wrote: Hi Tudor, 1. not sure, this is a more general question for people more familiar with surfaces and edits 2. nothing is necessary, however, if you have regions where you find difficulties in some subjects, I'd look at that region in all subjects (e.g. you mention the posterior end). Usually if surfaces on the base are good, the long should be high quality also. 3. looks good (I'd do space separated, also some columns merged in your email and fsid-base for subject3 is wrong). 4. using the two-stage model you could do a pairwise analysis between your groups in the second stage, so linear mixed effects model is not necessary. In the two stage model, just think of it as a cross sectional analysis of e.g. thickness change, instead of thickness. 5. yes, is sutiable. You'd have to run it several times, once for each of the measures you want to analyze. You can drop some of: --do-avg --do-rate --do-pc1 --do-spc --do-stack and only keep e.g. the rate or the pc1 (depending on what you want to analyze). You can also use --stack-rate to generate a stack of the rate maps. Best, Martin On 06/04/2014 01:19 PM, Tudor Popescu wrote: Hi Martin, I reran everything from scratch and this time the recons ended without error. Few more questions: 1) Is the brainmask.mgz vs wm.mgz problem that I described in my previous email (surfaces only starting to show rather late at the posterior end of some subjects) something that I need to correct (e.g., by editing wm.mgz), or is it fine as it is? 2) Given that I visually inspected all bases, Is it necessary to inspect all slices for the longitudinal overlaps (vols+surfs) of all subjects, or is it enough to just check the central coronal slice for each subject? I ask because it's not just opening freeview with all those layers that is very slow, but also navigating between slices 3) The tutorial covers the creation of long.qdec.table.dat for a single-group scenario; I have 3 groups, with scans on the first and final (fifth) day of training, and was wondering whether the following table looks correct fsid fsid-base group day ageDemeaned gender score subj1_day1 subj1 treatmentA 1 1.34 f 109 subj1_day5 subj1 treatmentA 5 1.34 f 109 subj2_day1 subj2 treatmentB 1 -5.85 m 102 subj2_day5 subj2 treatmentB 5 -5.85 m 102 subj3_day1 subj2 control 1 3.06 f 98 subj3_day5 subj2 control 5 3.06 f 98 4) Is this mixed design (3 groups and 2 time points, with both effect of group and of time being relevant) suitably analysed with only a simple 2 stage model, or is a linear mixed effects model necessary? Also, how are the stats different given there are 3 groups and not the usual 2 than most FS tutorials are based on? 5) Is the default long_mris_slopes command (which I understand does preliminary analyses, before going to QDEC) mentioned in the tutorial, i.e. long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage --sd $SUBJECTS_DIR suitable for my particular case? I will also look at surface area and lGI, so I suspect it's at least "--meas area" and "--meas lGI" that I need to add to the above command? Thanks so much! Tudor On 3 June 2014 02:02, Martin Reuter <mreuter(a)nmr.mgh.harvard.edu> wrote: HI Tudor, you can run the -long processes in parallel. Something else is wrong. Check if you have enough disk space. Re-run the long from scratch (to make sure everything is generated new). Best, Martin On Jun 2, 2014, at 5:34 PM, Tudor Popescu <tudor3(a)gmail.com> wrote: Hi Bruce I suspected this might be the case, since assessing 3D surfaces from a succession of 2D slices can be tricky, which is why I was wondering whether there's a better way to do these visual inspections. I checked those apparent artefacts in the other 2 planes (axial, saggital), but did not find it helpful in deciding whether the surfs was as they should or not. Something that I think is more likely to be a real problem (i.e., more than just a viewing plane disorientation), is that for many subjects, posterior slices only start to be followed by the surfaces quite late, e.g. from coronal slice 80 onward. This seems to be because those slices only appear in the brainmask.mgz, but not also in the wm.mgz (see screenshots attached). Also, after having run the cross and base steps, and ended up with folders of the type subj1_scanA, subj1_scanB etc, for the "long" step I launched simultaneously (for all subjects&scans) commands of the type recon-all -long subj1_scanA subj1 -all recon-all -long subj1_scanB subj1 -all however these resulted in two types of error messages: mghRead(/vols/Scratch/tpopescu/learning/FS/subj1_scanA.long.subj1/mri/aseg.mgz, -1): read error (those particular aseg.mgz files had size 0kB), and (standard_in) 2: Error: comparison in expression I initially had disk space issues, but after making space I relaunched the same commands with the -no-isrunning flag, but with the same results. Is it the case that the long commands for the different scans of a subject have to be launched sequentially rather than in parallel, i.e. the command for scanB should be run after the command for scanA has finished? Otherwise, what could the problem be? Thanks again for your help. Tudor On 1 June 2014 15:17, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: Hi Tudor are you assessing the thickness visually? If so, you are probably being misled by the orientation of the surface w.r.t. the viewing plane. Same fo the apparent bubbles. You need to look in a different orientation cheers Bruce On Sun, 1 Jun 2014, Tudor Popescu wrote: Many thanks Martin and Nick! The rendering option was already checked, but the freeview inspection commands were still very very slow, so I used commands of the following form, which as far as I understand should be equivalent: tkmedit subjID norm.mgz -surfs For several subjects (maybe 20 out of the total of 72), I noticed that the surfaces don\t seem to quite follow the GM/WM demarcation line as expected - for instance, by having portions of white surface (yellow line, see attached screenshots) surrounded by pial surface (red line), or by having very large cortical thickness in some parts of the brain. Is it possible that these apparent artefacts make sense "in context" (by looking at the adjacent slides), or is it the case that I need to go back and do white surface correction, and then redo all 3 steps of the longitudinal process? Thanks again for your help! Tudor On 29 May 2014 17:39, Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> wrote: Tudor, in your virtual machine, make sure the 3D rendering option, or 'use hardware rendering' (or something like that) is enabled. this would be on the Windows VM config side of things. otherwise it will do software rendering which is painfully slow. Nick > Hi Tudor, > > I don't think there is a way to speed things up. > Let me know if you find a case where the template is blurry or has > ghosts. It should not happen, but if it does it indicates a bad > registratration, you'd have to run the mri_robust_template command with > different parameters manually then. > > Best, Martin > > On 05/27/2014 06:13 PM, Tudor Popescu wrote: >> >> Hi Martin, >> Wasn't sure whether you'd seen my reply below, look forward to hear >> back your thoughts, thanks! >> Tudor >> >> On 25 May 2014 21:40, "Tudor Popescu" <tudor3(a)gmail.com >> <mailto:tudor3@gmail.com>> wrote: >> >> Thanks very much Martin and Bruce. I guess I'd misread the Wiki >> (my own fault, not the text's), and am glad to hear that the >> longitudinal pipeline is in fact perfectly suitable for my needs >> here. >> >> Having run the first 2 steps (cross and base), I'm a bit unclear >> how the output so far has to be manually inspected. It says in the >> tutorial >> <http://freesurfer.net/fswiki/FsTutorial/LongitudinalTutorial> >> that you should load each subject's base volume + surfs in >> freeview and then "move back and forth a few slices". However, >> even just loading each base in this manner takes ~1 min on my PC >> (CoreDuo, 4GB, Ubuntu Virtualbox in Windows 7), and then moving >> with PgUp/PgDn between all coronal slices (starting from the >> default slice=128, going all the way posterior and then all the >> way anterior) is excruciatingly slow. All of this would have to be >> repeated for all my 72 subjects - is there any way to optimise >> this manual inspection? >> >> Also, if the surfs turn out to not follow the volume correctly, >> presumably the thing to do is white surface correction + >> re-running recon. But what should one do if, due to an erroneous >> averaging between timepoints, you see blurs/ghosts in your base >> template? >> >> Many thanks! >> Tudor >> >> >> On 9 May 2014 21:33, Martin Reuter <mreuter(a)nmr.mgh.harvard.edu >> <mailto:mreuter@nmr.mgh.harvard.edu>> wrote: >> >> Hi Tudor, >> >> the longitudinal pipeline in FS is actually one of the best on >> the planet as far as I know :-). If there is any contradictory >> information on the wiki, can you point me to that so I can see >> what causes the misconception. Really: compared to independent >> processing, it significantly increases sensitivity. Also we >> have designed it to be unbiased with respect to a single time >> point or directionality. It is quite mature by now. >> >> You should definitely use the longitudinal pipeline for the >> analysis of your data. Now to your questions >> >> 1. QDEC: I am not too familiar with qdec. You can definitely >> try the 2-stage approach described on the wiki. There you >> first compute a measure of change (e.g. hippocampal volume >> change during your week) and then compare that measure across >> groups similar to a cross sectional volume/thickness analysis. >> You can also use our tools to run a linear mixed effects model >> if you want to do that (it is more involved and requires you >> to use matlab tools). In your case, you probably have 2 time >> points for all subjects and the time distance is probably the >> same for all subjects, so the 2-stage approach should be fine. >> >> 2. The image processing is done via the longitudinal pipeline >> (three steps: cross, base, long), to prepare the data look at >> the description of the 2-stage model >> http://freesurfer.net/fswiki/LongitudinalTwoStageModel >> and also the longitudinal tutorial >> http://freesurfer.net/fswiki/FsTutorial/LongitudinalTutorial >> >> 3. At the recon all level in FS you get (after the 3 steps) >> measurement for all time points. So you would compare those >> results across time in the stats. >> >> Hope that helps, Martin >> >> >> On 05/08/2014 08:14 AM, Tudor Popescu wrote: >>> Sorry for the repeat, wasn't sure whether this was received >>> the first time. >>> Tudor >>> >>> >>> On 6 May 2014 19:55, Tudor Popescu <tudor3(a)gmail.com >>> <mailto:tudor3@gmail.com>> wrote: >>> >>> Dear FS list, >>> >>> I have structural data from a learning study >>> (pre&post-training scans, with 3 groups). Although the >>> training was only one week, I'm guessing from an analysis >>> point of view, this still qualifies as longitudinal. I >>> want to check for >>> >>> * the main within-subjects effect of time point >>> (pre&post) >>> * the main between-subjects effect of group (treatment >>> A, treatment B, control), >>> * the time x group interaction >>> >>> I intend to look at thickness, surface area, volume, and >>> lGI. >>> >>> I read on the wiki >>> <http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing> >>> that FS is currently not optimal for longitudinal >>> analyses. I intend my FreeSurfer analysis to supplement a >>> VBM analysis done in FSL. In case it is in fact a good >>> idea to do this, my questions (not covered in the >>> 'longitudinal' wiki page) are: >>> >>> 1) Can QDEC be used for such an analysis, and if so, what >>> would be different as compared to a cross-sectional (no >>> temporal/within factor) study? >>> >>> 2) Also, is the pre-processing stage any different? >>> >>> 3) In FSL, for longitudinal designs you do stats on >>> images obtained as the difference between consecutive >>> time points. Does this have to be done in FreeSurfer as >>> well, and if so, is it done at the recon-all level or >>> only at the stats (QDEC) level? >>> >>> Thanks! >>> >>> Tudor >>> >>> >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> -- >> Martin Reuter, Ph.D. >> >> Instructor in Neurology >> Harvard Medical School >> Assistant in Neuroscience >> Dept. of Radiology, Massachusetts General Hospital >> Dept. of Neurology, Massachusetts General Hospital >> Research Affiliate >> Computer Science and Artificial Intelligence Lab, >> Dept. of Electrical Engineering and Computer Science, >> Massachusetts Institute of Technology >> >> A.A.Martinos Center for Biomedical Imaging >> 149 Thirteenth Street, Suite 2301 >> Charlestown, MA 02129 >> >> Phone:+1-617-724-5652 <tel:%2B1-617-724-5652> >> Email: >> mreuter(a)nmr.mgh.harvard.edu >> <mailto:mreuter@nmr.mgh.harvard.edu> >> reuter(a)mit.edu <mailto:reuter@mit.edu> >> Web :http://reuter.mit.edu >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> <mailto:Freesurfer@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 > > -- > Martin Reuter, Ph.D. > > Instructor in Neurology > Harvard Medical School > Assistant in Neuroscience > Dept. of Radiology, Massachusetts General Hospital > Dept. of Neurology, Massachusetts General Hospital > Research Affiliate > Computer Science and Artificial Intelligence Lab, > Dept. of Electrical Engineering and Computer Science, > Massachusetts Institute of Technology > > A.A.Martinos Center for Biomedical Imaging > 149 Thirteenth Street, Suite 2301 > Charlestown, MA 02129 > > Phone: +1-617-724-5652 > Email: > mreuter(a)nmr.mgh.harvard.edu > reuter(a)mit.edu > Web : http://reuter.mit.edu > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ 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. <02-06-2014, 22.17.45.png><02-06-2014, 22.17.55.png><only LH posterior.png><norm.png>_______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer --------------------------------- Dr. Martin Reuter Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreuter(a)nmr.mgh.harvard.edu reuter(a)mit.edu Web : http://reuter.mit.edu _______________________________________________ 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 -- Martin Reuter, Ph.D. Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreuter(a)nmr.mgh.harvard.edu reuter(a)mit.edu Web : http://reuter.mit.edu _______________________________________________ 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.

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possible to enable openmp with tracula cvsreg?
by Salil Soman 13 Jun '14

13 Jun '14

Hi, I noticed in the output for tracula -prep I am currently running using cvsreg it mentions openmp=1, I was wondering if there is a way to enable more than 1 core for openmp for tracula-prep? Thanks, -- Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System

2 1

trac-all -stat option
by Kathryn Cullen 13 Jun '14

13 Jun '14

Hello, I am trying to examine FA along the trajectory of the white matter tract, as described in the wiki: http://freesurfer.net/fswiki/FsTutorial/TraculaStatistics (half way down the page). I am using the FreeSurfer version 3.0. The wiki says: The pathstats.byvoxel.txt files will generally not contain the same number of positions (rows) for each subject because the tracts are reconstructed in each subject's native diffusion space and not in a template space. Thus they are not ready for performing group analyses yet. To combine these files from multiple subjects, interpolating the anisotropy and diffusivity values at corresponding positions along the tract for all subjects, run the following: trac-all -stat -c $TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial However, when I try to use the -stat option, it says it is not recognized. There is no -stat option described in the help, either. Am I using the wrong version, or do I need to upload something differently? Thanks very much, Katie -- Kathryn R. Cullen, M.D. Assistant Professor University of Minnesota Medical School Department of Psychiatry Division of Child and Adolescent Psychiatry F268 West Building 2450 Riverside Avenue Minneapolis, MN 55454 (612) 273-9762

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Re: [Freesurfer] Compatibility Tracula v.5.3 and recon v.5.2 longitudinal
by Anastasia Yendiki 13 Jun '14

13 Jun '14

Hi Yoon - If you are getting an error from longitudinal tracula, do check the tracula updates at the link that I gave you in my previous email. As for 5.2 recon-all, others can chime in here, but like I said it is not recommended to use it. Sorry about that. a.y On Thu, 22 May 2014, Yoonho Chung wrote: > Thanks for the quick response! > > If I already have all the T1 data processed using recon-all with FS v5.2, do you think it is okay to switch the stream to FS v.5.3 and run Tracula? - without having to do the recon-all again for the T1 data? It is because I am also experiencing DTI longitudinal error due to the OS issue (according to other threads). And if possible, I would like to avoid having to redo all the recons if we have to switch it to v5.3. > > Thanks again! > Yoon

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Re: [Freesurfer] Longitudinal design
by Martin Reuter 12 Jun '14

12 Jun '14

Hi Tudor. For the mri_concat command at the end, does it work when you run it directly? It should not. Are the input files there. Is the dimension correct (you can run mri info on them). Since they are just surface maps, just like thickness, their dimensions should agree (eith each other and with thickness, and number of vertices of surfaces). Best Martin Sent via my smartphone, please excuse brevity. -------- Original message -------- From: Tudor Popescu <tudor3(a)gmail.com> Date:06/07/2014 9:55 PM (GMT+01:00) To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Longitudinal design I should add that the commands for thickness, i.e. long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas thickness --hemi ?h --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time day --qcache fsaverage --sd $SUBJECTS_DIR finished without error, and for some reason, so did the surface area commands, when I ran them a second time. Also, I realised that for lGI, the flag for --meas was pial_lgi and not just lgi. However, the command long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas pial_lgi --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time day --qcache fsaverage --sd $SUBJECTS_DIR resulted in this error, similar for both hemispheres: SUBJECT F02 Stacking Within-Subject Maps mri_concat /vols/Scratch/tpopescu/learning/FS/F02_d1.long.F02/surf/rh.pial_lgi /vols/Scratch/tpopescu/learning/FS/F02_d5.long.F02/surf/rh.pial_lgi --o /vols/Scratch/tpopescu/learning/FS/F02/surf/rh.long.pial_lgi-stack.mgh ERROR 1 : mri_concat stacking did not work? Thanks again for your help! On 6 June 2014 17:45, Tudor Popescu <tudor3(a)gmail.com> wrote: Hi Martin, thanks a lot for your answers. The slopes command is giving me errors though, see below. I also attach the long.qdec.table.dat that I'm using. I should point out that those ?h.long.cortex.label files mentioned in the error messages are in fact at their expected locations, and appear to be fine (i.e. are not size 0) In case anyone else can advice about question 1, I'd be really grateful! Command Error long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas area --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time day --qcache fsaverage --sd $SUBJECTS_DIR No such file or directory mris_label_calc: could not open label file /vols/Scratch/tpopescu/learning/FS/F02/label/lh.long.cortex.label Invalid argument mris_label_calc: mris_label_calc.cpp:127: int main(int, char**): Assertion `l2 != __null' failed. long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas area --hemi rh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time day --qcache fsaverage --sd $SUBJECTS_DIR mris_calc: could not open label file /vols/Scratch/tpopescu/learning/FS/F23/label/rh.long.cortex.label Invalid argument mris_calc: could not read label file /vols/Scratch/tpopescu/learning/FS/F23/label/rh.long.cortex.label Invalid argument long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas lGI --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time day --qcache fsaverage --sd $SUBJECTS_DIR mris_label_calc: mris_label_calc.cpp:127: int main(int, char**): Assertion `l2 != __null' failed. SUBJECT F02 Intersecting Within-Subject Cortex Label cp /vols/Scratch/tpopescu/learning/FS/F02_d1.long.F02/label/lh.cortex.label /vols/Scratch/tpopescu/learning/FS/F02/label/lh.long.cortex.label mris_label_calc intersect /vols/Scratch/tpopescu/learning/FS/F02_d5.long.F02/label/lh.cortex.label /vols/Scratch/tpopescu/learning/FS/F02/label/lh.long.cortex.label /vols/Scratch/tpopescu/learning/FS/F02/label/lh.long.cortex.label ERROR -6 : mris_label_calc intersect did not work? long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas lGI --hemi rh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time day --qcache fsaverage --sd $SUBJECTS_DIR No such file or directory mris_label_calc: could not open label file /vols/Scratch/tpopescu/learning/FS/F02/label/rh.long.cortex.label Invalid argument mris_label_calc: mris_label_calc.cpp:127: int main(int, char**): Assertion `l2 != __null' failed. On 5 June 2014 16:00, Martin Reuter <mreuter(a)nmr.mgh.harvard.edu> wrote: Hi Tudor, 1. not sure, this is a more general question for people more familiar with surfaces and edits 2. nothing is necessary, however, if you have regions where you find difficulties in some subjects, I'd look at that region in all subjects (e.g. you mention the posterior end). Usually if surfaces on the base are good, the long should be high quality also. 3. looks good (I'd do space separated, also some columns merged in your email and fsid-base for subject3 is wrong). 4. using the two-stage model you could do a pairwise analysis between your groups in the second stage, so linear mixed effects model is not necessary. In the two stage model, just think of it as a cross sectional analysis of e.g. thickness change, instead of thickness. 5. yes, is sutiable. You'd have to run it several times, once for each of the measures you want to analyze. You can drop some of: --do-avg --do-rate --do-pc1 --do-spc --do-stack and only keep e.g. the rate or the pc1 (depending on what you want to analyze). You can also use --stack-rate to generate a stack of the rate maps. Best, Martin On 06/04/2014 01:19 PM, Tudor Popescu wrote: Hi Martin, I reran everything from scratch and this time the recons ended without error. Few more questions: 1) Is the brainmask.mgz vs wm.mgz problem that I described in my previous email (surfaces only starting to show rather late at the posterior end of some subjects) something that I need to correct (e.g., by editing wm.mgz), or is it fine as it is? 2) Given that I visually inspected all bases, Is it necessary to inspect all slices for the longitudinal overlaps (vols+surfs) of all subjects, or is it enough to just check the central coronal slice for each subject? I ask because it's not just opening freeview with all those layers that is very slow, but also navigating between slices 3) The tutorial covers the creation of long.qdec.table.dat for a single-group scenario; I have 3 groups, with scans on the first and final (fifth) day of training, and was wondering whether the following table looks correct fsid fsid-base group day ageDemeaned gender score subj1_day1 subj1 treatmentA 1 1.34 f 109 subj1_day5 subj1 treatmentA 5 1.34 f 109 subj2_day1 subj2 treatmentB 1 -5.85 m 102 subj2_day5 subj2 treatmentB 5 -5.85 m 102 subj3_day1 subj2 control 1 3.06 f 98 subj3_day5 subj2 control 5 3.06 f 98 4) Is this mixed design (3 groups and 2 time points, with both effect of group and of time being relevant) suitably analysed with only a simple 2 stage model, or is a linear mixed effects model necessary? Also, how are the stats different given there are 3 groups and not the usual 2 than most FS tutorials are based on? 5) Is the default long_mris_slopes command (which I understand does preliminary analyses, before going to QDEC) mentioned in the tutorial, i.e. long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage --sd $SUBJECTS_DIR suitable for my particular case? I will also look at surface area and lGI, so I suspect it's at least "--meas area" and "--meas lGI" that I need to add to the above command? Thanks so much! Tudor On 3 June 2014 02:02, Martin Reuter <mreuter(a)nmr.mgh.harvard.edu> wrote: HI Tudor, you can run the -long processes in parallel. Something else is wrong. Check if you have enough disk space. Re-run the long from scratch (to make sure everything is generated new). Best, Martin On Jun 2, 2014, at 5:34 PM, Tudor Popescu <tudor3(a)gmail.com> wrote: Hi Bruce I suspected this might be the case, since assessing 3D surfaces from a succession of 2D slices can be tricky, which is why I was wondering whether there's a better way to do these visual inspections. I checked those apparent artefacts in the other 2 planes (axial, saggital), but did not find it helpful in deciding whether the surfs was as they should or not. Something that I think is more likely to be a real problem (i.e., more than just a viewing plane disorientation), is that for many subjects, posterior slices only start to be followed by the surfaces quite late, e.g. from coronal slice 80 onward. This seems to be because those slices only appear in the brainmask.mgz, but not also in the wm.mgz (see screenshots attached). Also, after having run the cross and base steps, and ended up with folders of the type subj1_scanA, subj1_scanB etc, for the "long" step I launched simultaneously (for all subjects&scans) commands of the type recon-all -long subj1_scanA subj1 -all recon-all -long subj1_scanB subj1 -all however these resulted in two types of error messages: mghRead(/vols/Scratch/tpopescu/learning/FS/subj1_scanA.long.subj1/mri/aseg.mgz, -1): read error (those particular aseg.mgz files had size 0kB), and (standard_in) 2: Error: comparison in expression I initially had disk space issues, but after making space I relaunched the same commands with the -no-isrunning flag, but with the same results. Is it the case that the long commands for the different scans of a subject have to be launched sequentially rather than in parallel, i.e. the command for scanB should be run after the command for scanA has finished? Otherwise, what could the problem be? Thanks again for your help. Tudor On 1 June 2014 15:17, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: Hi Tudor are you assessing the thickness visually? If so, you are probably being misled by the orientation of the surface w.r.t. the viewing plane. Same fo the apparent bubbles. You need to look in a different orientation cheers Bruce On Sun, 1 Jun 2014, Tudor Popescu wrote: Many thanks Martin and Nick! The rendering option was already checked, but the freeview inspection commands were still very very slow, so I used commands of the following form, which as far as I understand should be equivalent: tkmedit subjID norm.mgz -surfs For several subjects (maybe 20 out of the total of 72), I noticed that the surfaces don\t seem to quite follow the GM/WM demarcation line as expected - for instance, by having portions of white surface (yellow line, see attached screenshots) surrounded by pial surface (red line), or by having very large cortical thickness in some parts of the brain. Is it possible that these apparent artefacts make sense "in context" (by looking at the adjacent slides), or is it the case that I need to go back and do white surface correction, and then redo all 3 steps of the longitudinal process? Thanks again for your help! Tudor On 29 May 2014 17:39, Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> wrote: Tudor, in your virtual machine, make sure the 3D rendering option, or 'use hardware rendering' (or something like that) is enabled. this would be on the Windows VM config side of things. otherwise it will do software rendering which is painfully slow. Nick > Hi Tudor, > > I don't think there is a way to speed things up. > Let me know if you find a case where the template is blurry or has > ghosts. It should not happen, but if it does it indicates a bad > registratration, you'd have to run the mri_robust_template command with > different parameters manually then. > > Best, Martin > > On 05/27/2014 06:13 PM, Tudor Popescu wrote: >> >> Hi Martin, >> Wasn't sure whether you'd seen my reply below, look forward to hear >> back your thoughts, thanks! >> Tudor >> >> On 25 May 2014 21:40, "Tudor Popescu" <tudor3(a)gmail.com >> <mailto:tudor3@gmail.com>> wrote: >> >> Thanks very much Martin and Bruce. I guess I'd misread the Wiki >> (my own fault, not the text's), and am glad to hear that the >> longitudinal pipeline is in fact perfectly suitable for my needs >> here. >> >> Having run the first 2 steps (cross and base), I'm a bit unclear >> how the output so far has to be manually inspected. It says in the >> tutorial >> <http://freesurfer.net/fswiki/FsTutorial/LongitudinalTutorial> >> that you should load each subject's base volume + surfs in >> freeview and then "move back and forth a few slices". However, >> even just loading each base in this manner takes ~1 min on my PC >> (CoreDuo, 4GB, Ubuntu Virtualbox in Windows 7), and then moving >> with PgUp/PgDn between all coronal slices (starting from the >> default slice=128, going all the way posterior and then all the >> way anterior) is excruciatingly slow. All of this would have to be >> repeated for all my 72 subjects - is there any way to optimise >> this manual inspection? >> >> Also, if the surfs turn out to not follow the volume correctly, >> presumably the thing to do is white surface correction + >> re-running recon. But what should one do if, due to an erroneous >> averaging between timepoints, you see blurs/ghosts in your base >> template? >> >> Many thanks! >> Tudor >> >> >> On 9 May 2014 21:33, Martin Reuter <mreuter(a)nmr.mgh.harvard.edu >> <mailto:mreuter@nmr.mgh.harvard.edu>> wrote: >> >> Hi Tudor, >> >> the longitudinal pipeline in FS is actually one of the best on >> the planet as far as I know :-). If there is any contradictory >> information on the wiki, can you point me to that so I can see >> what causes the misconception. Really: compared to independent >> processing, it significantly increases sensitivity. Also we >> have designed it to be unbiased with respect to a single time >> point or directionality. It is quite mature by now. >> >> You should definitely use the longitudinal pipeline for the >> analysis of your data. Now to your questions >> >> 1. QDEC: I am not too familiar with qdec. You can definitely >> try the 2-stage approach described on the wiki. There you >> first compute a measure of change (e.g. hippocampal volume >> change during your week) and then compare that measure across >> groups similar to a cross sectional volume/thickness analysis. >> You can also use our tools to run a linear mixed effects model >> if you want to do that (it is more involved and requires you >> to use matlab tools). In your case, you probably have 2 time >> points for all subjects and the time distance is probably the >> same for all subjects, so the 2-stage approach should be fine. >> >> 2. The image processing is done via the longitudinal pipeline >> (three steps: cross, base, long), to prepare the data look at >> the description of the 2-stage model >> http://freesurfer.net/fswiki/LongitudinalTwoStageModel >> and also the longitudinal tutorial >> http://freesurfer.net/fswiki/FsTutorial/LongitudinalTutorial >> >> 3. At the recon all level in FS you get (after the 3 steps) >> measurement for all time points. So you would compare those >> results across time in the stats. >> >> Hope that helps, Martin >> >> >> On 05/08/2014 08:14 AM, Tudor Popescu wrote: >>> Sorry for the repeat, wasn't sure whether this was received >>> the first time. >>> Tudor >>> >>> >>> On 6 May 2014 19:55, Tudor Popescu <tudor3(a)gmail.com >>> <mailto:tudor3@gmail.com>> wrote: >>> >>> Dear FS list, >>> >>> I have structural data from a learning study >>> (pre&post-training scans, with 3 groups). Although the >>> training was only one week, I'm guessing from an analysis >>> point of view, this still qualifies as longitudinal. I >>> want to check for >>> >>> * the main within-subjects effect of time point >>> (pre&post) >>> * the main between-subjects effect of group (treatment >>> A, treatment B, control), >>> * the time x group interaction >>> >>> I intend to look at thickness, surface area, volume, and >>> lGI. >>> >>> I read on the wiki >>> <http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing> >>> that FS is currently not optimal for longitudinal >>> analyses. I intend my FreeSurfer analysis to supplement a >>> VBM analysis done in FSL. In case it is in fact a good >>> idea to do this, my questions (not covered in the >>> 'longitudinal' wiki page) are: >>> >>> 1) Can QDEC be used for such an analysis, and if so, what >>> would be different as compared to a cross-sectional (no >>> temporal/within factor) study? >>> >>> 2) Also, is the pre-processing stage any different? >>> >>> 3) In FSL, for longitudinal designs you do stats on >>> images obtained as the difference between consecutive >>> time points. Does this have to be done in FreeSurfer as >>> well, and if so, is it done at the recon-all level or >>> only at the stats (QDEC) level? >>> >>> Thanks! >>> >>> Tudor >>> >>> >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> -- >> Martin Reuter, Ph.D. >> >> Instructor in Neurology >> Harvard Medical School >> Assistant in Neuroscience >> Dept. of Radiology, Massachusetts General Hospital >> Dept. of Neurology, Massachusetts General Hospital >> Research Affiliate >> Computer Science and Artificial Intelligence Lab, >> Dept. of Electrical Engineering and Computer Science, >> Massachusetts Institute of Technology >> >> A.A.Martinos Center for Biomedical Imaging >> 149 Thirteenth Street, Suite 2301 >> Charlestown, MA 02129 >> >> Phone:+1-617-724-5652 <tel:%2B1-617-724-5652> >> Email: >> mreuter(a)nmr.mgh.harvard.edu >> <mailto:mreuter@nmr.mgh.harvard.edu> >> reuter(a)mit.edu <mailto:reuter@mit.edu> >> Web :http://reuter.mit.edu >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> <mailto:Freesurfer@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 > > -- > Martin Reuter, Ph.D. > > Instructor in Neurology > Harvard Medical School > Assistant in Neuroscience > Dept. of Radiology, Massachusetts General Hospital > Dept. of Neurology, Massachusetts General Hospital > Research Affiliate > Computer Science and Artificial Intelligence Lab, > Dept. of Electrical Engineering and Computer Science, > Massachusetts Institute of Technology > > A.A.Martinos Center for Biomedical Imaging > 149 Thirteenth Street, Suite 2301 > Charlestown, MA 02129 > > Phone: +1-617-724-5652 > Email: > mreuter(a)nmr.mgh.harvard.edu > reuter(a)mit.edu > Web : http://reuter.mit.edu > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ 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. <02-06-2014, 22.17.45.png><02-06-2014, 22.17.55.png><only LH posterior.png><norm.png>_______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer --------------------------------- Dr. Martin Reuter Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreuter(a)nmr.mgh.harvard.edu reuter(a)mit.edu Web : http://reuter.mit.edu _______________________________________________ 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 -- Martin Reuter, Ph.D. Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreuter(a)nmr.mgh.harvard.edu reuter(a)mit.edu Web : http://reuter.mit.edu _______________________________________________ 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.

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