Freesurfer October 2012

freesurfer@nmr.mgh.harvard.edu

119 participants
191 discussions

FW: TRACULA some fiber volumes being too small
by Fernando Ventrice 28 Nov '12

28 Nov '12

Dear Freesurfer/Tracula users, Finally I could successfully test Tracula and I think it is amazing what it can do automatically. These are the commands I used: export FREESURFER_HOME=${HOME}/Programs/freesurfer_510 && source $FREESURFER_HOME/SetUpFreeSurfer.sh source /etc/fsl/fsl.sh export FSLPARALLEL=condor trac-all -prep -c /home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/dmrirc_Fernando_Ventrice trac-all -bedp -c /home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/dmrirc_Fernando_Ventrice # "trac-all -bedp" gave some errors so I used bedpostx directly: bedpostx /home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/20120112_VENTRICE_FERNANDO/dmri trac-all -path -c /home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/dmrirc_Fernando_Ventrice freeview -tv /home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/20120112_VENTRICE_FERNANDO/dpath/merged_avg33_mni_flt.mgz -v /home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/20120112_VENTRICE_FERNANDO/dmri/dtifit_FA.nii.gz & All finished without errors, but there seems to be a problem with CC Forceps Mayor volume, which gave very small values. Is this OK or I made some mistake? First I tested with some patient and other fiber tracks also gave very small volumes. I attached some pictures and the dmrirc and trac-all log files. Best, Fernando Ventrice El contenido del presente mensaje y el de sus adjuntos, es confidencial, privado y de uso exclusivo de los destinatarios a los cuales está dirigido, pudiendo contener información legalmente protegida. Queda prohibida la revisión, divulgación, publicación, modificación, copia, distribución o acción en relación con esta información, por personas o entidades distintas al destinatario. Si usted, por alguna razón, lo ha recibido por error, por favor tenga la amabilidad de eliminarlo de su sistema. Las opiniones contenidas, son exclusivas de su autor, y no representa necesariamente, la opinión de FLENI. http://www.fleni.org.ar

3 6

Fw:contrast matrix
by Meng Li 13 Nov '12

13 Nov '12

Hi Freesurfer experts, I'm very sorry to bother you, but I am very confused with the following questions: My experimental design includes 3 discrete factors: diagnosis with two levels (A, B); genotype with two levels (G, T); gender (F, M), and two covariates. So I can get 8 classes: AGF, AGM, ATF,ATM, BGF, BGM, BTF, BTM. 1) I want to perform 2 (diagnosis)* 2(genotype) interaction analysis with regressing out the effect of gender and two covariates, but I don't know the rules for setting the contrasts for the interaction. The contrast matrix I used is: 0.25 0.25 -0.25 -0.25 -0.25 -0.25 0.25 0.25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 is it correct? If it is correct, how to explain the results, for example, what does the positive (or negative) clusters stand for? Or the clusters showed in the t-test statistical map are the regions that have the significant interaction? 2) When I perform the main effect of dignosis, is the following matrix I used correct? 0.25 0.25 0.25 0.25 -0.25 -0.25 -0.25 -0.25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 (I think it regressed out the effect of genotype and gender, that is it takes the genotype as a covariable) Or I should create another fsgd file, that has 4 classes: AF, AM, BF, BM. And I can use the matrix (0.5 0.5 -0.5 -0.5 0 0 0 0 0 0 0 0) to perform the main effect of diagnosis. which one is right? Any help will be very appreciated. Best wishes, Meng Li

2 2

Surface-based normalization, smoothing and averaging
by Shigetoshi Takaya 08 Nov '12

08 Nov '12

Dear Freesurfer experts, I would like to have your help. I have a volume data of a certain parameter on white/grey matter boundary (X.nii). What I want to do are as follows: Step 1: I want to register it onto a standard space using surface-based alignment and smooth it. Step 2: I want to generate the averaged images of several subjects on the standard inflated surface. My questions are follows: Q1) For Step 1, I guess I need to convert the image using mri_vol2surf (X.nii --> X.mgh), then use mri_surf2surf and mris_smooth. If it is the case what should I use for <target subject name> for mri_sur2surf? Q2) How to do Step 2? Thanks in advance, Shige

2 1

Compiling on Linux PPC
by Tony Dale 01 Nov '12

01 Nov '12

Hi, Does anyone have any advice for compiling freesurfer on Linux powerPC architectures? I've managed to compile a 64-bit version of freesurfer on Linux PowerPC, and I'd be happy to post the documentation for the compile process I used - if I could be sure it would build usable binaries :-( So far, the compiled binaries run in to some fairly basic problems with opening DICOM files. Here's an example using mri_probedicom with the debugging cranked up, trying to open a file that opens fine using the precompiled x86 mri_probedicom binary: # mri_probedicom --i /tmp/s003/E16002S003I00001.dcm DCM Dump Elements Object type: UNKNOWN Object size: 132 DCM Dump Elements Complete Starting DCM_CloseObject DCM_CloseObject: Legal object and file closed 0008 0005 CS 0 000008 ID Specific Character Set newElementItem: CTN_MALLOC 0 152 36214390 5349 5f4f UN 0 000010 newElementItem: CTN_MALLOC 0 152 36214430 3030 0008 UN 0 000018 newElementItem: CTN_MALLOC 0 152 36214540 DCM Dump Elements Object type: ELEMENT LIST Object size: 24 Group: 0008, Length: 8 0008 0005 0 // ID Specific Character Set// Group: 5349, Length: 8 5349 5f4f 0 // //DCM Dump Elements Complete Starting DCM_CloseObject DCM_CloseObject: Legal object and file closed DCM_CloseObject: group 0008 DCM_CloseObject: Element 00080005 DCM_CloseObject: free 36214390 DCM_CloseObject: group 5349 DCM_CloseObject: Element 53495f4f DCM_CloseObject: free 36214430 0800 0500 UN 0 000008 newElementItem: CTN_MALLOC 0 152 36214390 4953 4f5f UN 0 000010 newElementItem: CTN_MALLOC 0 152 36214430 3030 0800 UN 0 000018 newElementItem: CTN_MALLOC 0 152 36214540 DCM Dump Elements Object type: ELEMENT LIST Object size: 24 Group: 0800, Length: 8 0800 0500 0 // //Group: 4953, Length: 8 4953 4f5f 0 // //DCM Dump Elements Complete Starting DCM_CloseObject DCM_CloseObject: Legal object and file closed DCM_CloseObject: group 0800 DCM_CloseObject: Element 08000500 DCM_CloseObject: free 36214390 DCM_CloseObject: group 4953 DCM_CloseObject: Element 49534f5f DCM_CloseObject: free 36214430 Starting DCM_CloseObject ERROR: /tmp/s003/E16002S003I00001.dcm is not a dicom file or some other problem Entering IsDICOM (/tmp/s003/E16002S003I00001.dcm) Opening /tmp/s003/E16002S003I00001.dcm as part10 DCM Dump Elements Object type: UNKNOWN Object size: 132 DCM Dump Elements Complete DCM_FILEOPENFAILED 20092 DCM failed to open file: /tmp/s003/E16002S003I00001.dcm in DCM_OpenFile Starting DCM_CloseObject DCM_CloseObject: Legal object and file closed Opening as littleendian 0008 0005 CS 0 000008 ID Specific Character Set newElementItem: CTN_MALLOC 0 152 36214640 5349 5f4f UN 0 000010 newElementItem: CTN_MALLOC 0 152 36214710 3030 0008 UN 0 000018 newElementItem: CTN_MALLOC 0 152 36214820 DCM Dump Elements Object type: ELEMENT LIST Object size: 24 Group: 0008, Length: 8 0008 0005 0 // ID Specific Character Set// Group: 5349, Length: 8 5349 5f4f 0 // //DCM Dump Elements Complete DCM_FILEOPENFAILED Starting DCM_CloseObject DCM_CloseObject: Legal object and file closed DCM_CloseObject: group 0008 DCM_CloseObject: Element 00080005 DCM_CloseObject: free 36214640 DCM_CloseObject: group 5349 DCM_CloseObject: Element 53495f4f DCM_CloseObject: free 36214710 Opening as bigendian 0800 0500 UN 0 000008 newElementItem: CTN_MALLOC 0 152 36214640 4953 4f5f UN 0 000010 newElementItem: CTN_MALLOC 0 152 36214710 3030 0800 UN 0 000018 newElementItem: CTN_MALLOC 0 152 36214820 DCM Dump Elements Object type: ELEMENT LIST Object size: 24 Group: 0800, Length: 8 0800 0500 0 // //Group: 4953, Length: 8 4953 4f5f 0 // //DCM Dump Elements Complete DCM_FILEOPENFAILED Starting DCM_CloseObject DCM_CloseObject: Legal object and file closed DCM_CloseObject: group 0800 DCM_CloseObject: Element 08000500 DCM_CloseObject: free 36214640 DCM_CloseObject: group 4953 DCM_CloseObject: Element 49534f5f DCM_CloseObject: free 36214710 Opening as format conversion DCM_ILLEGALOPTION Starting DCM_CloseObject Leaving IsDICOM (/tmp/s003/E16002S003I00001.dcm) ERROR: /tmp/s003/E16002S003I00001.dcm is not a dicom file or some other problem This email may be confidential and subject to legal privilege, it may not reflect the views of the University of Canterbury, and it is not guaranteed to be virus free. If you are not an intended recipient, please notify the sender immediately and erase all copies of the message and any attachments. Please refer to http://www.canterbury.ac.nz/emaildisclaimer for more information.

2 2

recon-all finished with ERRORs
by Christine Smith 01 Nov '12

01 Nov '12

See my original post at the end of this message and some more information included below. What would have been edited between the previous run without errors and the current run with errors is the brainmask, the wm.mgz file, and control points. On Tue, Oct 30, 2012 at 1:21 PM, Christine Smith <cnsmith(a)ucsd.edu> wrote: > Here it is: > > New invocation of recon-all > > Thu Oct 4 03:52:22 PDT 2012 > /usr/local/mridata/D_New_Patient/Lobe_Analysis/CON1 > /usr/local/freesurfer/bin/recon-all > -s /usr/local/mridata/D_New_Patient/Lobe_Analysis/CON1 -calabel > #-------------------------------------- > #@# SubCort Seg Thu Oct 4 03:52:22 PDT 2012 > > mri_seg_diff --seg1 aseg.auto.mgz --seg2 aseg.mgz --diff aseg.manedit.mgz > > Linux squirelab.ucsd.edu 2.6.18-308.13.1.el5 #1 SMP Tue Aug 21 > 18:44:22 EDT 2012 x86_64 x86_64 x86_64 GNU/Linux > > recon-all -s CON1 exited with ERRORS at Thu Oct 4 03:52:22 PDT 2012 > > On Tue, Oct 30, 2012 at 12:45 PM, Bruce Fischl > <fischl(a)nmr.mgh.harvard.edu> wrote: >> what were the last 20 lines or so of the recon-all.log? >> >> On Tue, 30 Oct 2012, Christine Smith wrote: >> >>> Hello, >>> >>> After successfully running a subject through freesurfer (recon-all >>> -make all) several times as I fixed some pial and white matter edits, >>> I now get the message that recon-all finished with errors. Inspection >>> of the recon-all.log doesn't reveal any error messages to me in any >>> particular step. >>> >>> What should I be looking for to track down the reason that errors were >>> generated? >>> >>> I already examined the talairach transform and that looks great. >>> I loaded the pial and white matter surfaces and they look fine. The >>> segmentation aparc+aseg looks great too. >>> >>> Thanks, >>> Christine >>> >>> >>

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Re: [Freesurfer] fieldsign-sess problem in retinotopy
by Zhou, Wei 31 Oct '12

31 Oct '12

Hi, Doug Thank you for your reply. I have tried exporting SUBJECTS_DIR to the directory of upper fold, retinotopy or SUBJ01 But none of them works. Still the same error msg. So what should SUBJECTS_DIR be exported to for this analysis? Best Wei >Hi Wei, this is a bug in the error msg. It is trying to say that your >source subject is not in the $SUBJECTS_DIR. >doug >On 10/27/2012 02:27 PM, Zhou, Wei wrote: > Dear freesurfers, > > I am trying retinotopy analysis in freesurfer. For "fieldsign-sess", I > encounter the following problem when I type "fieldsign-sess -a > rtopy.self.lh -occip -s SUBJ01" or "fieldsign-sess -a rtopy.self.lh > -occip -sf sessid": > > */media/users/zhouw4/testf/retinotopy/SUBJ01/log/fieldsign-sess.log* > *subject: Undefined variable.* > > my structure of retinotopy fold is : > retinotopy > | |--sessid > |--SUBJ01 > |--subjectname > > |--bold > |--001 > |--f.nii > |--rtopy.par| > > I really appreciate it if you could give me some idea about that > problem. Thanks a lot in advance. > > Best > Wei Zhou > Medical Physics Ph.D. Student > Diagnostic Imaging Track > cgxz...(a)gmail.com <mailto:cgxz...@gmail.com> > zho...(a)livemail.uthscsa.edu <mailto:zho...@livemail.uthscsa.edu> > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

2 1

Error during recon-all with notal-check on
by Darshan P 31 Oct '12

31 Oct '12

I have a MRI data which has a lesion on the left side . recon-all fails with errors . I was hoping to recover from this error . The last few lines of the log file is as follows'

1 1

Re: [Freesurfer] FW: TRACULA some fiber volumes being too small
by Anastasia Yendiki 31 Oct '12

31 Oct '12

If FSL isn't happy with the directions, that's going to be fatal b/c trac-all relies on bedpostx running properly. I'm going to look into this further to try to figure out what it is about this data that's causing the discrepancy. On Wed, 31 Oct 2012, Fernando Ventrice wrote: > Dear Anastasia, > When I open the dtifit_V1 and dtifit_FA with Freeview the vector directions actually are OK, but when I open them with FSLview they are similar to your screen-shot. Here I also send a screen-shot with the comparison between the two softwares in each monitor. > Best, > Fernando > ________________________________________ > From: Anastasia Yendiki [ayendiki(a)nmr.mgh.harvard.edu] > Sent: Tuesday, October 30, 2012 1:24 PM > To: Fernando Ventrice > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] FW: TRACULA some fiber volumes being too small > > See screenshot now :) > > On Tue, 30 Oct 2012, Anastasia Yendiki wrote: > >> >> Hi Fernando - Thanks for uploading your data. Looking at the primary >> directions from tensor fit on the data that you sent me (see screenshot), >> they seem to be off by a 90 degree angle from what you'd expect them. This >> means that your gradient table is probably off as well. >> >> Hope this helps, >> a.y >> >> On Thu, 18 Oct 2012, Fernando Ventrice wrote: >> >>> Dear Freesurfer/Tracula users, >>> Finally I could successfully test Tracula and I think it is amazing what >>> it can do automatically. These are the commands I used: >>> >>> export FREESURFER_HOME=${HOME}/Programs/freesurfer_510 && source >>> $FREESURFER_HOME/SetUpFreeSurfer.sh >>> source /etc/fsl/fsl.sh >>> export FSLPARALLEL=condor >>> trac-all -prep -c >>> /home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/dmrirc_Fernando_Ventrice >>> trac-all -bedp -c >>> /home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/dmrirc_Fernando_Ventrice >>> # "trac-all -bedp" gave some errors so I used bedpostx directly: >>> bedpostx >>> /home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/20120112_VENTRICE_FERNANDO/dmri >>> trac-all -path -c >>> /home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/dmrirc_Fernando_Ventrice >>> freeview -tv >>> /home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/20120112_VENTRICE_FERNANDO/dpath/merged_avg33_mni_flt.mgz >>> -v >>> /home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/20120112_VENTRICE_FERNANDO/dmri/dtifit_FA.nii.gz >>> & >>> >>> All finished without errors, but there seems to be a problem with CC >>> Forceps Mayor volume, which gave very small values. Is this OK or I made >>> some mistake? First I tested with some patient and other fiber tracks also >>> gave very small volumes. I attached some pictures and the dmrirc and >>> trac-all log files. >>> Best, >>> Fernando Ventrice >>> >>> El contenido del presente mensaje y el de sus adjuntos, es confidencial, >>> privado y de uso exclusivo de los destinatarios a los cuales está >>> dirigido, pudiendo contener información legalmente protegida. Queda >>> prohibida la revisión, divulgación, publicación, modificación, copia, >>> distribución o acción en relación con esta información, por personas o >>> entidades distintas al destinatario. Si usted, por alguna razón, lo ha >>> recibido por error, por favor tenga la amabilidad de eliminarlo de su >>> sistema. Las opiniones contenidas, son exclusivas de su autor, y no >>> representa necesariamente, la opinión de FLENI. >>> http://www.fleni.org.ar >>> >> > > > 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. > > El contenido del presente mensaje y el de sus adjuntos, es confidencial, privado y de uso exclusivo de los destinatarios a los cuales está dirigido, pudiendo contener información legalmente protegida. Queda prohibida la revisión, divulgación, publicación, modificación, copia, distribución o acción en relación con esta información, por personas o entidades distintas al destinatario. Si usted, por alguna razón, lo ha recibido por error, por favor tenga la amabilidad de eliminarlo de su sistema. Las opiniones contenidas, son exclusivas de su autor, y no representa necesariamente, la opinión de FLENI. > http://www.fleni.org.ar > > El contenido del presente mensaje y el de sus adjuntos, es confidencial, privado y de uso exclusivo de los destinatarios a los cuales está dirigido, pudiendo contener información legalmente protegida. Queda prohibida la revisión, divulgación, publicación, modificación, copia, distribución o acción en relación con esta información, por personas o entidades distintas al destinatario. Si usted, por alguna razón, lo ha recibido por error, por favor tenga la amabilidad de eliminarlo de su sistema. Las opiniones contenidas, son exclusivas de su autor, y no representa necesariamente, la opinión de FLENI. > http://www.fleni.org.ar >

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Re: [Freesurfer] average measure of cortical thickness
by Bruce Fischl 31 Oct '12

31 Oct '12

yes, I think so Bruce On Tue, 30 Oct 2012, Daniel Ferreira wrote: > So, as a measure of whole brain cortical thickness average is it better to > "Mean Thickness" from aparc.stats file? > > > 2012/10/30 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Hi Daniel > > the parcellations are not uniform in size, and therefore the > average of them will not be the same as averaging over the > cortex. > > cheers > Bruce > On Tue, 30 Oct 2012, Daniel Ferreira wrote: > > Hi, > I was wondering what should I use as an average of > cortical thickness for > the whole cortex. > > The aparc.stats output gives a value of "Mean > Thickness" for each > hemisphere. But this value does not coincide with > the one I get if I average > the 34 variables from aparc.stats. Do you know why? > > thanks so much in advance > > Daniel > > > > > 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. > > > >

3 4

SPM VBM and Freesurfer group analysis
by Infinity 31 Oct '12

31 Oct '12

Hi, I did a SPM VBM (using dartel) analysis as well as a freesurfer group analysis. After correcting for multiple comparisons. Both maps give me pretty different results. From the literature review both sets of results make sense but the fact that the results don't agree is troubling me. I have checked everything multiple times and still get the same results. Is it common that the two methods give different results? I also wanted to know the interpretation of the surface measures that freesurfer reports, especially the curv and sulc measures. What does it mean exactly when two groups have different sulc or curv measures? In my results I get a negative correlation between curv measure and volume measure in the same region. So in that region for curv measure group1 > group 2 while in the same region for the volume measure group1 < group2. How exactly is the curv measure related to volume and area measures? Is there a standard reference where all the details for these measures are mentioned? Thank you.

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Freesurfer October 2012