Freesurfer January 2017

freesurfer@nmr.mgh.harvard.edu

123 participants
215 discussions

Cerebral (without ventricles) Volume = aseg.stats / SupraTentorialNotVent ?
by Kaiming Yin 21 Feb '17

21 Feb '17

Dear guys, Could I ask which value in the stats/aseg.stats represents the volume of the cerebrum (including the subcortical structures while excluding the ventricles and brain stem)? I'm not sure whether the "SupraTentorialNotVent" can be the value for this measurement, and could it be a bit bigger than the real value due to the partial volume effect? Besides, could I also ask is there a value represent the volume of the cerebellum? Currently I calculate the volume by adding the left/right cerebellar GM/WM values in the detailed list in aseg.stats file. Many thanks, Kaiming

2 3

Analysis of rates or percent changes
by Katarina Trojacanec 14 Feb '17

14 Feb '17

Hi, I have a question about the analysis of rates or percent changes. I use data with available scans at baseline (TP1) and the 6-month (TP2), 12-month (TP3) and 24-month (TP4) follow-ups from ADNI dataset. An example of some of the data in the appropriate qdec table is given below: fsid fsid-base years age weight diagnosis gender Glob_CDR NPI-Q_TotScr MMSE_TotScr FAQ_TotScr visit1_2_3_4 ADNI_sub1_sc ADNI_base1 0 81.3 y AD M x x x x sc ADNI_sub1_m06 ADNI_base1 0.528767123 81.9 y AD M x x x x m06 ADNI_sub1_m12 ADNI_base1 1.030136986 82.4 y AD M x x x x m12 ADNI_sub1_m24 ADNI_base1 2.030136986 83.4 y AD M x x x x m24 ADNI_sub2_sc ADNI_base2 0 74 y AD F x x x x sc ADNI_sub2_m06 ADNI_base2 0.501369863 74.5 y AD F x x x x m06 ADNI_sub2_m12 ADNI_base2 1.005479452 75 y AD F x x x x m12 ADNI_sub2_m24 ADNI_base2 2 76 y AD F x x x x m24 The base is constructed using all four time points. The time variable is given in years. I am using long_stats_slopes for aseg.stats as follows: long_stats_slopes --qdec ./qdec/long_AD_NL_TP1_2_3_4.qdec.table.dat --stats aseg.stats --meas volume --sd $SUBJECTS_DIR --do-avg --do-rate --do-pc1fit --do-pc1 --do-spc --do-stack --generic-time --time years --stack-avg ./qdec/long_AD_NL_TP1_2_3_4 (similarly for ?h.aparc.stats) Having in mind that TP1 and TP2, as well as TP2 and TP3 are separated approximately 6 months and TP3 and TP4 are separated approximately 12 months, are the annualized percent change or atrophy rates using this scenario reasonable (statistically?). Is it maybe more reasonable to apply the same scenario using three time points (for example TP1, TP3 and TP4 from the previous example and the template based only on these time points with the same approximate difference between all of them of 12 months, or TP1, TP2 and TP3 from the previous example and the template based only on these time points with the same approximate difference between all of them of 6 months)? Best Regards, Katarina Trojacanec, M.Sc. Teaching and research assistant Faculty of Computer Science and Engineering Ss. Cyril and Methodius University - Skopje, Republic of Macedonia

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recon-all -localGI with longitudinal pipeline output
by Mihaela Stefan 09 Feb '17

09 Feb '17

Hello FreeSurfers, I am trying to run recon-all -s <subjID> -localGI on a longitudinal dataset but I get this error: ERROR: Are you trying to run or re-run a longitudinal time point? If so, please specify the following parameters: \' -long <tpNid> <templateid> \' where <tpNid> is the time point id (SAME as cross sectional ID) and <templateid> is the ID created in the -base run. The directory <tpNid>.long.<templateid> will be created automatically or used for output, if it already exists. Do I really need these if I want to run -localGI or for some reason recon-all thinks that I am trying to re-run the longitudinal pipeline? I renamed the folder replacing "long" (e.g. *OAS2_0001_MR1.new.OAS2_0001 instead of **OAS2_0001_MR1.long.OAS2_0001* ) and recon-all -localGI seems to work. Is there a better way to do this? Thanks! Mihaela

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Edits to Aseg in the Longitudinal Stream
by Tamara Tavares 09 Feb '17

09 Feb '17

Hello, After I make edits to my aseg output in the longitudinal stream, do I just run the following command to recreate the final volumes: recon-long -autorecon2-noaseg -subjid <Subj_ID> I assume the -subjid is the name of the edited time point and <Subj_ID> is the name of the recreated volumes? Thank you, Tamara

2 1

Longitudinal stream with v6 but cross with v5.3
by Matthieu Vanhoutte 09 Feb '17

09 Feb '17

Dear FS's experts, I have run all my cross with v5.3 and hesitate to run all longitudinal process with v6. Does that make sense and will improve the process or would it be risky to do this ? Many thanks for your lights ! Best regards, Matthieu

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Command for Reverse Normalizing with mri_vol2vol Using CVS m3z Morphs
by Douglas Merkitch 03 Feb '17

03 Feb '17

Hello Freesurfer experts, >From your wiki page, I understand how to normalize volumes in subject diffusion space to the CVS template: mri_vol2vol --targ $FREESURFER_HOME/subjects/cvs_avg35/mri/norm.mgz \ --m3z $SUBJECTS_DIR/$subj/cvs/combined_tocvs_avg35_elreg_afteraseg-norm.m3z \ --noDefM3zPath --reg $TUTORIAL_DIR/$subj/dtrecon/register.dat \ --mov fa-masked.mgz \ --o fa-masked.ANAT+CVS-to-avg35.mgz \ --interp trilin --no-save-reg However, how would one take take a volume in CVS template space and reverse normalize it back to subject diffusion space? Is this possible? If so, what would that command look like and what other steps would be necessary to get the required inputs? Thanks, Doug Douglas Merkitch Neurological Sciences Rush University Medical Center Email: Douglas_Merkitch(a)rush.edu<mailto:Douglas_Merkitch@rush.edu>

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longitudinal tracula error
by Bárbara Avelar Pereira 02 Feb '17

02 Feb '17

Dear FreeSurfer experts, I’m running tracula on longitudinal data but I’ve encountered the following error at the “trac-all -prep” stage: ERROR: flag ; unrecognized (see below) trac-preproc -c /Documents/TRACULA/TEST/S0001.01_T1/scripts/dmrirc.local -log /Documents/TRACULA/TEST/S0001.01_T1/scripts/trac-all.log -cmd /Documents/TRACULA/TEST/S0001.01_T1/scripts/trac-all.cmd ; trac-preproc -c /Documents/TRACULA/TEST/S0001.01_T2/scripts/dmrirc.local -log /Documents/TRACULA/TEST/S0001.01_T2/scripts/trac-all.log -cmd /Documents/TRACULA/TEST/S0001.01_T2/scripts/trac-all.cmd ; trac-preproc -c /Documents/TRACULA/TEST/S0001.01/scripts/dmrirc.local -log /Documents/TRACULA/TEST/S0001.01/scripts/trac-all.log -cmd /Documents/TRACULA/TEST/S0001.01/scripts/trac-all.cmd ; ERROR: flag ; unrecognized As an example, I defined the parameters in my dmrirc file as: set subjlist = ( S0001.01_T1 \ S0001.01_T2 \ S0004.00_T1 \ S0004.00_T2 ) set baselist = ( S0001.01 \ S0001.01 \ S0004.00 \ S0004.00 ) set dcmlist = ( S0001.01_T1/DTI.nii \ S0001.01_T2/DTI.nii \ S0004.00_T1/DTI.nii \ S0004.00_T2/DTI.nii ) From the mailing list, it seems a similar issue has been fixed in previous updates but I have tried both version 5.3 and 6.0 and still get this error... My tracula directory contains 3 directories per participant: 2 with the *.long.* output for timepoint 1 and 2, and a directory with the base. Including the base gives the error above, but if I take it out, it asks for it: ERROR: cannot find /Documents/TRACULA/TEST/S0001.01 From what I understand, the base is not necessary to run any analysis, but it has to be there anyhow (?): https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg45332.html Maybe I am understanding this incorrectly? Since the base is used to create the longitudinal output (*long*), including the aparc+aseg.mgz file, and those are then used in tracula, I thought I could run things without it. I decided to take out the “set baselist” part from the configuration file — this way it seems to run fine (so far). But I assume it’s there for a reason so I’m not sure this is a solution at all... Any help would be much appreciated! Details: 1) freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 2) platform: CentOS release 6.8 (Final) 3) Operating system details (kernel name, release, version, etc.): Linux 2.6.32-642.11.1.el6.x86_64 #1 SMP Fri Nov 18 19:25:05 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux

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Cortical thickness from ROI in volume format
by Martin Juneja 01 Feb '17

01 Feb '17

Hi FreeSurfer experts, My goal is to extract cortical thickness of several ROIs, which are in volume space. I am following instructions from this page: https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness My ROIs and T1 image are in the form of binary mask and are already in same standard space (MNIT1.nii). So following the instructions, I am able to perform until step 3 (I created registration file X.dat using fslregister command to register MNIT1.nii with fslaverage). After that I am using this command: tksurfer fsaverage lh inflated -overlay lh.fsaverage.ROI5.mgh -fthresh 0.5 to make sure that the ROI in surface format is at correct place. But after I run this command I do not see the region anywhere on surface. I tried to view it using FreeView also, its giving me attached image. From FreeView it looks like the ROI is now a brain mask and is all over the brain with a constant value everywhere. I am not sure why this is happening. Next, I have 26 ROIs, 12 on left hemisphere, 12 on right hemisphere and 2 in the midline. Somehow, 11/12 ROIs on left hemisphere and 2 ROIs in the midline are working fine when I view those in tksurfer or FreeView but rest all are showing me value of 1 all over the brain. For left hemisphere and midline ROIs, I am using exactly same steps as mentioned in the instructions but for right hemisphere, I just replaced 'lh' with 'rh' in step 3. Any help would be really appreciated.

2 3

QDEC - Controlling for gender
by Jennifer Szeto 01 Feb '17

01 Feb '17

Hi Freesurfer experts, I am trying to compare cortical thickness between groups while controlling for age and gender using QDEC. However, gender is not showing up as a covariate variable or a nuisance factor (only showing up as a fixed factor), I am wondering how I could control for gender in this case? Thank you very much, Jen

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flip4fsl missing in stable6
by Fan, Qiuyun 31 Jan '17

31 Jan '17

Hi FreeSurfer experts, I figured 'flip4fsl' is missing from /usr/local/freesurfer/stable6/bin/. Can someone help to make a copy from /usr/local/freesurfer/stable5_3_0/bin/flip4fsl, if possible? Thanks a lot! Best, Qiuyun

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Freesurfer January 2017