Freesurfer

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30132 discussions

Getting started with Freesurfer on Windows
by Trietsch, Rayna 10 May '12

10 May '12

Hi, I am a research assistant and I'm new to Freesurfer. I am using Windows and downloaded the VirtualBox and Freesurfer. I was able to get through the steps on the website for "Testing Freesurfer". However, I get stuck when I am trying to download the sample data for the tutorials. In the directions for downloading the sample data, it tells you to find a directory with 100GB of space. How do I do that? It seems to me that there is no area in my directory which has any where near that much room. The computer which I am running on has over 800G free but I don't see how that relates to the terminal which I am using in VirtualBox. I am not familiar with Linux so I am doing my best to figure it out but I just can't see to find a way to download the data for the tutorials. Any help would be much appreciated. Thank you very much. ~Rayna~

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DOSS, thresholding and thresh-sign questions
by Reem Jan 10 May '12

10 May '12

Dear all I'm fairly new to Freesufer and have started a cortical thickness group analysis. I had a few doubts/questions which I found most the answers for on previous emails on the FS archives - thank you! But I have a few more questions, I hope one of the FS experts can help me out. I will briefly describe my analysis - I have 2 groups - controls and patients. I am interested in the simple questions - do controls have higher GM thickness than patients and where? Do patients have higher GM thickness than controls and where? I expect controls to have higher GM thickness than the patients in cortical areas, but I expect the patients to have higher volumes of certain subcortical structures. I am not interested in the effects of age or gender on GM thickness although I would like to control for these as covariates of no interest. In the example below I have not considered gender for simplicity's sake. Because I assume a similar slope among both groups, I decided to go with DOSS and not DODS. I set out my FSGD file as below: GroupDescriptorFile 1 Title lh.group_age.glmdir MeasurementName thickness Class Control Class Patient Variables age Input Subject_02 Control 29 Input Subject_04 Control 22 Input Subject_05 Control 23 Input Subject_06 Control 29 Input Subject_07 Control 18 Input Subject_08 Control 20 Input Subject_09 Control 36 Input Subject_10 Control 24 Input Subject_14 Control 29 Input Subject_15 Control 26 Input Subject_16 Control 39 Input Subject_17 Control 40 Input Subject_18 Control 26 Input Subject_19 Control 44 Input Subject_20 Control 34 Input Subject_22 Control 28 Input Subject_23 Control 26 Input Subject_31 Control 46 Input Subject_32 Control 40 Input Subject_41 Control 38 Input Subject_01 Patient 35 Input Subject_03 Patient 28 Input Subject_11 Patient 46 Input Subject_12 Patient 22 Input Subject_21 Patient 32 Input Subject_25 Patient 33 Input Subject_26 Patient 40 Input Subject_27 Patient 30 Input Subject_28 Patient 31 Input Subject_29 Patient 42 Input Subject_30 Patient 39 Input Subject_33 Patient 43 Input Subject_34 Patient 44 Input Subject_35 Patient 36 Input Subject_36 Patient 32 Input Subject_37 Patient 37 Input Subject_38 Patient 27 And my contrast files as: lh-diff-ControlvsPatient.mtx: +1 -1 0 0 lh-diff-PatientvsControl.mtx: -1 1 0 0 For GLM analysis I used the following command: "mri_glmfit --y lh.group_age.10.mgh --fsgd lh.group.fsgd doss --C lh-diff-ControlvsPatient.mtx --surf fsaverage lh --cortex --glmdir lh.group_age.glmdir" My questions are: Surface-based group analysis: 1. Can I ignore the error message: 'WARNING: unrecognized mri_glmfit cmd option doss' 2. Do I need 2 contrasts as above or should I be running only the first contrast with the 'abs' thresh-sign in order to obtain a double-sided t-test? 3. If my alternative hypothesis is that Controls>Patients and I specify a 'negative' thresh-sign - does that mean I will only see clusters where Controls<Patients (the reverse of my contrast)? The command I run is "mri_glmfit-sim --glmdir lh.group_age_precachedsim.glmdir--cache 1.3 neg" 4. I'm a bit confused about the vertex-wise threshold - if I specify it to be 3 (p=0.001), is that more or less stringent than specifying it to be 1.3 (p=0.05). I thought that the later (p=0.05) would allow for the consideration of more vertices and therefore would be less stringent, however when I applied both to try and test my theory, no clusters survived multiple comparison correction with p=0.05 but 1 cluster survived when I specified p=0.001. Could someone please shed some light on this? Subcortical volume group analysis: 1. Can I just perform statistics in a program such as SPSS on the subcortical structure volumes I obtain from the 'aseg.stats' file within each subject's stats sub-directory? Or are there other steps that need to be undertaken in FS beforehand? I'm sorry about the long email, I really appreciate your advice so thank you in advance Kind regards Reem Reem Jan BPharm (Hons), RegPharmNZ PhD Student / Pharmacist School of Pharmacy, Faculty of Medical & Health Sciences, The University of Auckland, Private Bag 92019, Auckland, New Zealand. Ph: +64 9 373 7599 ext 81138. DDI: +64 9 923 1138 F: +64 9 367 7192

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Re: [Freesurfer] Qdec 1.4 Error
by Nick Schmansky 10 May '12

10 May '12

anson, check the terminal output after you press the 'generate stats table' button. it gives a more succinct error message. when this function fails, its almost always because an aseg.stats file for one of the subjects is missing or corrupt. you can regenerate the aseg.stats for a subject by: recon-all -s subjid -segstats nick > Hi everyone, > > I ran recon-all and qcache ran successfully as well. > > Now I am getting this error in qdec v1.4 when I try to generate stats > data table (see attached) > > I also attached one subjects aseg.stats file if that helps. > > I remember seeing another error indicating (file too small, but I think my > $SUBJECTS_DIR was not set correctly that time. > > Qdec.table.dat loaded in fine, but it seems I am missing some files? > > Any suggestions? > > Best wishes > > Anson K. > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should not > be used for urgent or sensitive issues > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Poor Cortical Reconstructions in Pediatrics
by Xin Zhang 10 May '12

10 May '12

Hello FreeSurfers, Please ignore the previous email. This one includes an example picture. We are processing about 100 pediatric subjects ages 3-9 using FreeSurfer 5.1.0. For some reason, in about 25 of the subject, the right supramarginal, right middletemporal, and superiortemporal regions have poor cortical reconstructions. After reviewing the raw scans, we do not see any reason why these regions would be poorly segmentated. Can anyone give us any feedback for why these regions are reconstructing poorly? Our only ideas are that our subject ages might be causing issues, or normalizing the minor brightness gradient could be causing issues (although the poor segmentations occur even on subjects that have no brightness gradient on their raw scans). Thank you very much, Xin

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Qdec 1.4 Error
by Kairys, Anson 10 May '12

10 May '12

Hi everyone, I ran recon-all and –qcache ran successfully as well. Now I am getting this error in qdec v1.4 when I try to “generate stats data table” (see attached) I also attached one subjects aseg.stats file if that helps. I remember seeing another error indicating (file too small, but I think my $SUBJECTS_DIR was not set correctly that time. Qdec.table.dat loaded in fine, but it seems I am missing some files? Any suggestions? Best wishes Anson K. ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

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Re: [Freesurfer] optseq2 and tnullmin/max
by Hanah Chapman 10 May '12

10 May '12

Hi Doug, Thank you for the quick response. I tried the new file, and it fixes the problem with the tnullmax. However, I'm still having trouble computing the right number of tp. If I want a null after every event, that's 96 nulls. If I set the tnullmax/min range at 4-10s, then nulls will have an average duration of 7s, so 96 * 7/2 = 336 tp, plus 96 tp for the stimuli, = 432 tp. But with 432 tp I get a "could not enforce tnullmax" error. Oddly, with a lower ntp (384), I don't get an error, but get extra time at the end (so one null at the end of 70s). Evidently I'm not computing the ntp correctly. Alternatively, could I just cut the final null even down to the right length? Thanks again, Hanah > Hi Hanah, I just found and fixed the bug. It was making the effective > tNullMax = tNullMin + your specified tNullMax. I've put a new (linux) > version here: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/optseq2.linux > doug > > > On 05/09/2012 06:09 PM, Chapman, Hanah wrote: > > Dear list, > > > > I have an optseq2 question, and would very much appreciate your time. > > > > I'm having difficulty calculating the required number of timepoints. > > I'd like to use --tnullmin and --tnullmax so as to have a null event > > in between each trial, with a duration of 4-8 sec. I have 16 > > conditions, 6 repeats/run, 2s trials, 2s TR. I computed that a run > > would need 16*6 = 96 timepoints for the trials. Then there would be 96 > > null events (to have one between each trial), so with an average 6s > > duration for nulls, a run needs 96*6/2 = 288 timepoints for the nulls, > > so 96+288 = 384 tp total. However, when I run optseq2 with these > > parameters, I still get nulls that are longer than 8s, and there is > > evidently extra time left over, since the last null event is 70 sec > > long. I'm using the following code: > > > > --ntp 384 --tr 2 --psdwin 0 20 --tnullmin 4 --tnullmax 8 --nkeep 6 > > --o outfile --nsearch 1000 \ > > --ev DD 2 6 \ > > --ev DF 2 6 \ > > --ev DP 2 6 \ > > --ev DN 2 6 \ > > --ev FF 2 6 \ > > --ev FD 2 6 \ > > --ev FN 2 6 \ > > --ev FP 2 6 \ > > --ev PP 2 6 \ > > --ev PD 2 6 \ > > --ev PN 2 6 \ > > --ev PF 2 6 \ > > --ev NN 2 6 \ > > --ev ND 2 6 \ > > --ev NF 2 6 \ > > --ev NP 2 6 > > > > I understand that the 4-8s range may be too tight, and relaxing it is > > not a big deal. However, I tried 4-10s, and still has the problems > > with nulls > 10s and extra time at the end. > > > > Thank you for your time, > > > > Hanah Chapman > > Postdoctoral Fellow > > The Ohio State University > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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TRACULA niftii file
by Gabor Perlaki 10 May '12

10 May '12

Dear all, Is TRACULA able to handle 4D FSL niftii as input for DTI images? Are bves/bvalues extracted by dcm2nii and MRICro accurate for TRACULA? I think TRACULA needs the bvecs in the image coordinate system, which is not the same as scanner coordinate system in case of oblique acquisition. Do I need to use dcm2nii with correction for slice angulation to compensate for the image plane. The DTI was acquired on a Simenes TRIO with the standard Siemens DTI sequence (ep2diff), not the MGH DTI sequence. Software version: VB17A Does anybody have any experience with TRACULA and Siemens DTI? Thanks, Gabor

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Re: [Freesurfer] Error with recon-all
by Ed Gronenschild 10 May '12

10 May '12

Hi Nick, Apologies, I should have looked at the recon-all.log file myself. It says that there was an error with mris_topo_fixer: it couldn't allocate memory (malloc error). So I guess that the brainmask is still not correct. I will try to fix that with the option -wsmore. Cheers, Ed On 9 May 2012, at 18:53, Nick Schmansky wrote: > can you send the recon-all.log file? does it say why the > lh.orig_corrected file wasnt created? > > On Wed, 2012-05-09 at 09:56 +0200, Ed Gronenschild wrote: >> Hi, >> >> I'm using the version of recon-all that Nick provided >> at April 17 to be able to run nu_correct prior to the >> Talairach stage. (I'm on a Mac, OSX 10.6, version >> v5.1.0). The command given was >> >> recon-all -autorecon-all -hippo-subfileds -no-wsgcaatlas \ >> -clean-tal -s subject. >> >> recon-all stopped and issued the following error: >> >> cp: ../surf/lh.orig_corrected: No such file or directory. >> >> Note that I included the option -no-wsgcaatlas to get >> a better skullstripping because in the default mode >> the skulltripping was bad. With this option it looks >> good. >> I got the above error regularly for other subjects as well >> and by including the -no-wsgcaatlas option recon-all >> finished without error, except for the present case. >> >> Cheers, >> Ed >> _______________________________________________ >> 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.

2 1

recon-all error
by Rashmi Singh 09 May '12

09 May '12

Hello, I ran recon –all on my scans and the output files reported the following error: SUBJECTS_DIR /home/rsingh/storage/labs/pbellgowan/MTBI/RASHMIANALYSIS/Check-Long/GE/FreeSurfer FREESURFER_HOME /opt/freesurfer Loading source label. Invalid argument ERROR reading /home/rsingh/storage/labs/pbellgowan/MTBI/RASHMIANALYSIS/Check-Long/GE/FreeSurfer/fsaverage/label/lh.BA1.label Linux dale 2.6.32-40-server #87-Ubuntu SMP Tue Mar 6 02:10:02 UTC 2012 x86_64 GNU/Linux recon-all -s AA435.C1 exited with ERRORS at Wed May 9 01:37:19 CDT 2012. I couldn't locate the folder fsaverage: /home/rsingh/storage/labs/pbellgowan/MTBI/RASHMIANALYSIS/Check-Long/GE/FreeSurfer/fsaverage Please advise. Rashmi. ________________________________ This document may contain information covered under the Privacy Act, 5 USC 552(a), and/or the Health Insurance Portability and Accountability Act (PL 104-191) and its various implementing regulations and must be protected in accordance with those provisions. Healthcare information is personal and sensitive and must be treated accordingly. If this correspondence contains healthcare information it is being provided to you after appropriate authorization from the patient or under circumstances that don't require patient authorization. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Redisclosure without additional patient consent or as permitted by law is prohibited. Unauthorized redisclosure or failure to maintain confidentiality subjects you to application of appropriate sanction. If you have received this correspondence in error, please notify the sender at once and destroy any copies you have made.

2 1

optseq2 and tnullmin/max
by Chapman, Hanah 09 May '12

09 May '12

Dear list, I have an optseq2 question, and would very much appreciate your time. I'm having difficulty calculating the required number of timepoints. I'd like to use --tnullmin and --tnullmax so as to have a null event in between each trial, with a duration of 4-8 sec. I have 16 conditions, 6 repeats/run, 2s trials, 2s TR. I computed that a run would need 16*6 = 96 timepoints for the trials. Then there would be 96 null events (to have one between each trial), so with an average 6s duration for nulls, a run needs 96*6/2 = 288 timepoints for the nulls, so 96+288 = 384 tp total. However, when I run optseq2 with these parameters, I still get nulls that are longer than 8s, and there is evidently extra time left over, since the last null event is 70 sec long. I'm using the following code: --ntp 384 --tr 2 --psdwin 0 20 --tnullmin 4 --tnullmax 8 --nkeep 6 --o outfile --nsearch 1000 \ --ev DD 2 6 \ --ev DF 2 6 \ --ev DP 2 6 \ --ev DN 2 6 \ --ev FF 2 6 \ --ev FD 2 6 \ --ev FN 2 6 \ --ev FP 2 6 \ --ev PP 2 6 \ --ev PD 2 6 \ --ev PN 2 6 \ --ev PF 2 6 \ --ev NN 2 6 \ --ev ND 2 6 \ --ev NF 2 6 \ --ev NP 2 6 I understand that the 4-8s range may be too tight, and relaxing it is not a big deal. However, I tried 4-10s, and still has the problems with nulls > 10s and extra time at the end. Thank you for your time, Hanah Chapman Postdoctoral Fellow The Ohio State University

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