Freesurfer

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30089 discussions

tkregister2 wrong orientation
by Yosuke Morishima 11 May '12

11 May '12

Dear Freesurfer specialits, I now have a problem that tkregister2 gives wrong orientation, specifically L-R orientation is flipped. I'm trying surface DTI fiber tracking by using FSL and Freesurfer as described in FSL documentation below and using tkregister2 to obtain transformation matrix from Freesurfer space to structural space. http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_surface.html I got transformation matrix with the following command. tkregister2 --mov mri/orig.mgz --targ mri/rawavg.mgz --regheader --reg junk --fslregout freesurfer2struct.mat --noedit Apply this transformation matrix (freesurfer2struct.mat) to a freesurfer-space image, and then I got L-R flipped image in structural space. I would really appreciate if you have any suggestions to solve the problem. Thanks. Best wishes, Yosuke Here is the message appeared in the terminal. tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl target volume /home/yosuke/oldhdd/DTI/freesurf/subject/sub00/mri/rawavg.mgz movable volume /home/yosuke/oldhdd/DTI/freesurf/subject/sub00/mri/orig.mgz reg file junk LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /home/yosuke/oldhdd/DTI/freesurf/subject/sub00/mri/rawavg.mgz INFO: target does not conform to COR format, so I'm going to reslice to COR. This will not affect the final registration. Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /home/yosuke/oldhdd/DTI/freesurf/subject/sub00/mri/orig.mgz Tmov: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 1.000 -0.000 -0.000 -0.000; -0.000 1.000 0.000 0.000; -0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 -0.000 -0.000 -0.000; -0.000 1.000 0.000 0.000; -0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; Determinant 1 subject = subject-unknown RegMat --------------------------- -1.000 0.002 -0.004 -0.000; 0.003 -0.162 -0.987 0.000; 0.003 0.987 -0.162 -0.000; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTIGZ -- ------------------------------------------------------ Yosuke Morishima M.D. Ph.D. Laboratory for Social and Neural Systems Research Institute for Empirical Research in Economics University of Zurich Blumlisalpstrasse 10 CH-8006, Zurich Switzerland Phone: +41 44 634 51 69 Fax: +41 44 634 49 07 Email yosukemorishima(a)gmail.com

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Coordinates does not match after mri_convert
by Yong Wook Shin 11 May '12

11 May '12

Hi I converted a diffusion image from BRIK into nii formats using mri_convert (for example, mri_convert -it brik -ot nii original.BRIK converted.nii) and found the two images, original BRIK and converted nii had different coordinates as following. original one: R-to-L extent: -119.855 [R] -to- 118.270 [L] -step- 1.875 mm [128 voxels] A-to-P extent: -165.576 [A] -to- 72.549 [P] -step- 1.875 mm [128 voxels] I-to-S extent: -102.099 [I] -to- 41.901 [S] -step- 4.000 mm [ 37 voxels] converted one: R-to-L extent: -118.917 [R] -to- 119.208 [L] -step- 1.875 mm [128 voxels] A-to-P extent: -71.612 [A] -to- 166.513 [P] -step- 1.875 mm [128 voxels] I-to-S extent: -100.099 [I] -to- 43.901 [S] -step- 4.000 mm [ 37 voxels] I could not find any similar issue on the mailing list. Best, Yong Yong-Wook Shin MD. PhD. Assistant Professor ASAN Medical Center Department of Psychiatry, Ulsan University School of Medicine, 86 Asanbyeongwon-gil, Songpa-gu, Seoul, 138-736, Republic of Korea shaman_korea(a)mac.com

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Re: [Freesurfer] DOSS, thresholding and thresh-sign questions
by Reem Jan 10 May '12

10 May '12

Hi Doug Thank you very much for answering all my questions, I hope it's okay that I ask for further clarification on one point "clusterwise correction is probably more reliable at higher voxel-wise thresholds". Can I clarify what is meant by 'higher' in this context i.e. Higher = more significant and therefore a lower p value e.g. 0.0001 is higher than 0.05 OR Higher = higher p value and therefore less significant e.g. 0.05 is higher than 0.0001 Sorry about the simplicity of the question, I just wanted to make sure I'm interpreting your advice correctly. Many thanks again Kind regards Reem Hi Reem, #1. Is this from mri_glmfit-sim? If so, you can ignore it #2. You do not need both contrasts. Use abs to get a double sided test #3. The first contrast will be positive for Control>Patient. If you specify neg, it will only show clusters where Control<Patient #4. Depends on what you mean by "stringent". There is nothing more or less conservative about any particular voxel-wise threshold since you are not drawing conclusions based on the voxel-wise threshold but on the cluster-wise p-value. In general, the clusterwise correction is probably more reliable at higher voxel-wise thresholds. Subcortical: yes, just create a table and load it into SPSS. The only other thing is that you may want to normalize the volumes for ICV or brain volume, depending upon your hypothesis. doug On 05/09/2012 08:44 PM, Reem Jan wrote: > > 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 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] problems with analysis after using fslmaths
by Douglas N Greve 10 May '12

10 May '12

What frequencies did you chose for the FSL bandpass filter? What is you mkanalysis-sess command? On 05/07/2012 02:58 PM, Caspar M. Schwiedrzik wrote: > yes > > 2012/5/7 Douglas N Greve <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > Did you regenerate the seeds after filtering? > > > On 05/07/2012 02:50 PM, Caspar M. Schwiedrzik wrote: > > I have tried analyses with only one seed time course (either 1 > voxel, mean of a sphere of 1 voxel radius, or mean of a > functionally defined roi), as well as several seeds within the > same design matrix, with the same problem. > All of these analyses did yield higher pcc when done without > filtering. > Caspar > > 2012/5/7 Douglas N Greve <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard. edu > <mailto:greve@nmr.mgh.harvard.edu>>> > > > Is this doing all of those seeds simultaneously or one seed > at a time? > > On 05/07/2012 02:25 PM, Caspar M. Schwiedrzik wrote: > > Hi, > > I am trying to use fslmaths to filter my data before I plug it > into a > > resting state analysis. However, once I obtain a pcc map, all > > correlation coefficients are <0.1, even the autocorrelation > with the > > seed voxel. > > The data look fine when I open them in Matlab using MRIread; the > > correlations between individual voxel time courses obtained in > Matlab > > is about 0.6. > > > > My analysis stream is as follows: > > a) I filter the data using "fslmaths input -bptf highpass > lowpass > > output"; from this I obtain a filtered nii.gz file > > b) I extract a seed timecourse from the filtered data in Matlab > > c) I run mkanalysis-sess with -notask > > d) I run selxavg3-sess > > e) I overlay the pcc.nii > > > > I have tried this with smoothed and unsmoothed data, with and > without > > nuisance regressors, with different seeds, with mri_convert > after step > > a. It is not a problem with the overlay since the max values > in pcc > > are all <0.1. > > I noticed that there are some differences in the nifti header > (as read > > with MRIread) before and after filtering, but it seemed to > me that > > they are gone after I used mri_convert. > > I do find much higher correlations with unfiltered data. > > Any advice what could be going wrong here? I am using > Freesurfer 5.1 > > and FSL 4.1.9 on Linux. > > Thanks, Caspar > > > > > > > > ______________________________ _________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh. harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > https://mail.nmr.mgh.harvard. edu/mailman/listinfo/ > freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard. edu > <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/ fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh. harvard.edu/fswiki/ BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> > FileDrop: www.nmr.mgh.harvard.edu/ > facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard. edu/facility/filedrop/index. html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> > > ______________________________ _________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh. harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard. edu/mailman/listinfo/ freesurfer > <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 > <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. > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/ fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/ facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] bbregister for fmri FEAT data
by Erlend Hodneland 10 May '12

10 May '12

Hi again Yes, test.nii is the functional data registered to the anatomy. The following files have now been uploaded to your filedrop and can be downloaded by the email account "gr...(a)nmr.mgh.harvard.edu" 1. vol0001.nii.gz : functional input 2. orig.mgz : anatomical target 3. register-test.dat : Output Freesurfer registration file 4. test.nii : Output functional data registered to anatomy Thank you for helping us, Erlend And the functional is test.nii.gz? If so, can you upload vol0001.nii.gz, register-test.dat, test.nii.gz, and orig.mgz to our file drop? doug On 04/25/2012 07:49 AM, Erlend Hodneland wrote: > Both the fmri data registered to orig is mismatched, and also the original > raw fmri data are mismatched with orig, > see the link here showing our raw data (fmri, orig and 152MNI) shown in > fslview > > http://vedlegg.uib.no/?id=297a1242fa82b4b7565b470806254c5a > > > It is orig.nii converted from orig.mgz that we show yes. > > Erlend > > > What images are mismatched? Specifically, which anatomical image are you > loading into fslview? > If you have not loaded the orig.mgz (converted to nii), then there will be be > a > mismatch. > doug > > > > On 04/24/2012 04:29 AM, Erlend Hodneland wrote: > > Hi again, > > > > We are trying to do the same as was done in Trachtenberg et al 2012 > > (Neurobiology of Aging), ie opt.the commonly used FLIRT+FNIRT registration > > in > > FEAT with BBreg: > > > > "For group analysis, functional data were registered, via the high > > resolution > > anatomical image, to the Montreal Neurological Institute (MNI) standard > > brain. Functional data were aligned to the anatomical image initially using > > FMRIB's Linear Image Registration Tool, (FLIRT) ([Jenkinson and Smith, > > 2001] > > <http://www.sciencedirect.com/science/article/pii/S0197458010004926#bib27> > > and[Jenkinson et al., 2002] > > > > <http://www.sciencedirect.com/science/article/pii/S0197458010004926#bib28>), > > then optimized using the Boundary-Based Registration (BBR) approach (Greve > > and Fischl, 2009 > > > > <http://www.sciencedirect.com/science/article/pii/S0197458010004926#bib21>). > > Registration from anatomical to standard space was carried out using > > FMRIB’s > > Non-Linear Image Registration Tool (FNIRT)." > > > > > > That is, flirt from fmri --> brain, then initializing bbregister fmri --> > > brain by the previous flirt registration, then flirt and fnirt from brain > > --> > > standard space and finally fmri --> standard space and putting all these > > transformations together. > > > > > > However, our images are orientad as follows from top -> bottom (fmri, > > orig, > > 152MNI): > > > > http://vedlegg.uib.no/?id=297a1242fa82b4b7565b470806254c5a > > > > As shown in the previous communication, when we directly apply the images > > to > > the registration the results are oriented incorrectly, as the input images. > > > > Can you recommend a specific solution to overcome the orientation mismatch > > in > > these images which is compatible with the registration tasks? > > > > > > Thank you for your patience and help! > > > > > > All best > > > > E.H. > > > > > > Hi Erlend, while the images in the tkregister2 pics are oriented > > correctly the registration is way off. What images are you loading into > > fslview? You'll need to convert the orig.mgz into nii and load that to > > check the registration. > > doug > > > > On 04/22/2012 04:16 AM, Erlend Hodneland wrote: > > > Hi again, > > > > > > the registration looks fine in tkregister2, but is apparently wrong in > > > fslview (and also mricron). See the attached files (as link from > > > http://vedlegg.uib.no/?id=399ad2cce1a3138f8eb4f6a06f4acfc4) showing > > > screenshots of fslview and tkregister2. How can this be explained, and > > > how can we visualize the correct orientation in fslview? > > > What does this misalignment influence any further processing with > > > fnirt and concatenation of the affine transformation fields? > > > > > > This is our command we run for bbregister: > > > > > > bbregister --s subj_505 --mov vol0001.nii.gz --reg register-test.dat > > > --init-fsl --t2 --o test.nii.gz > > > > > > where vol0001 is the first volume in the fmri sequence and is flipped > > > to align with LAS (as the highres). > > > > > > Thank you for your kind help, > > > > > > Erlend Hodneland > > > > > > ean that it is in the wrong orientation? It should be in > > > the same orientation as the anatomical. How does the reg look in > > > tkregister2? Note that fslview can display volumes in odd orientations > > > even when the orientation is correct. > > > doug > > > > > > On 04/13/2012 03:31 AM, Erlend Hodneland wrote: > > > > Hi, > > > > > > > > we are trying to register fmri FEAT data (example_func.nii) to the > > > > anatomical scan (processed in Freesurfer) using bbregister to > > opt. > > > > the affine registration before running FNIRT. > > > > > > > > However, the orientation of the registered image is flipped > > around and > > > > is incorrect after applying bbregister. > > > > > > > > We have tried: > > > > > > > > 1) bbregister --s subj_501 --mov example_func.nii.gz --reg > > > > register.dat --init-header --bold --o example_func2highres-fs.nii > > > > 2) bbregister --s subj_501 --mov example_func.nii.gz --reg > > > > register.dat --init-fsl --bold --o example_func2highres-fs.nii > > > > 3) bbregister --s subj_501 --o example_func2highres-fs.nii > > --feat > > > > "myfeatdirectory" > > > > 4) tkregister2 --mov example_func.nii --regheader --reg tkreg.dat > > > > (this one looks correct) > > > > followed by > > > > bbregister --s subj_501 --mov example_func.nii.gz --reg > > register.dat > > > > --init-reg tkreg.dat --bold --o example_func2highres-fs.nii > > > > > > > > 5) reorienting to match the highres: > > > > > > > > fslorient -swaporient example_func > > > > fslswapdim example_func x -y z example_func_swap (correct > > > > orientation) > > > > > > > > followed by > > > > bbregister --s subj_501 --mov example_func_swap.nii.gz --reg > > > > register.dat --init-fsl --bold --o > > example_func_swap2highres-fs.nii > > > > > > > > with the output being flipped in wrong orientation for all > > options. > > > > > > > > We would greatly appreciate if you have any suggestions for how to > > > > overcome this problem! > > > > > > > > Cheers/Sincerly/All best > > > > > > > > Erlend Hodneland

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update to the virtualbox image
by eric porges 10 May '12

10 May '12

I have successfully installed and launched the virualbox freesurfer image, but I am unable to update it and I need to install smbfs in order to access my data. The address that this installation points to appears to no longer supported ubuntu. We have replicated this problem on two local PCs. Is there a chance that the image you provide could be updated? Thank you

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Creating new label in one hemi based on region in another hemi
by Stephen Politzer-Ahles 10 May '12

10 May '12

Hello, I have created a region in the left hemisphere by selecting my own set of vertices (based on functional data). I would like to also create a region as similar as possible in the right hemisphere. Does Freesurfer provide any functions to create a right-hemisphere region (label) using a corresponding left-hemisphere region as input? Thank you, Steve Politzer-Ahles -- Stephen Politzer-Ahles University of Kansas Linguistics Department http://www.linguistics.ku.edu/

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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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