Freesurfer July 2012

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hippo_subfields questions
by Gabriel Gonzalez Escamilla 19 Jul '12

19 Jul '12

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Automated sub-region segmentation - Amygdala
by Marc Rudolph 18 Jul '12

18 Jul '12

Good afternoon, I am new to freesurfer - is it possible to auto-segment the Amygdala into sub-regions? Thank you for your time, Marc

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mni152.register.dat
by Garikoitz Lerma Usabiaga 18 Jul '12

18 Jul '12

Hi freesurfer experts, I want to use a volume based MNI152 ROI in Freesurfer, when I check it over fsaverage with the following command the ROI is not in the correct position...: tkmedit fsaverage T1.mgz -overlay ROI45.nii -overlay-reg $FREESURFER_HOME/average/mni152.register.dat And I have the same problem when I convert it to surface: cd $SUBJECTS_DIR/fsaverage/surf mri_vol2surf \ --mov ../../ROI2/ROI45.nii \ --reg $FREESURFER_HOME/average/mni152.register.dat \ --projdist-max 0 1 0.1 \ --interp nearest \ --hemi lh \ --out lh.fsaverage.ROI45.mgh \ --reshape - Is this a correct way of using it? Should I get proper results or I am missing anything? and, - Does it make sense creating a new fsaverage using the /spm8/canonical/avg152T1.nii, then applying the ROI which is already in 152 space, and referring the cortical thickness of all the subjects to this "new fsaverage"? (the functional analysis is being carried in SPM as well). Many thanks for your answers, Gari

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Re: [Freesurfer] multiple comparisons correction
by Meng Li 18 Jul '12

18 Jul '12

Dear professor, Thanks for your reply. You said that when drawing conclusions from both hemispheres then I need to use .025, but I found that in qdec interface, the default value of -cwpvalue is 0.05. So are they inconsistent? I also want to find a solution about an ERROR. I tried to run a cortical thickness analysis to look for differences between two groups (patients and controls) with regressing out the gender factor, the patients group have 1 female and 17 male, after analysis, I got the results. But when I add another continuous variable as covariate, I received the message: "ERROR: matrix is ill-conditioned or badly scaled." Then I tried to change the gender composition the patients groups: 2 female/16 male, and the problem was solved. so is it right about what i did, or I need another way to solve this problem? Thanks, Best wishes Meng On 07/06/2012 10:00 PM, Meng Li wrote: > Hi, freesurfer expert, > I performed the statistical analysis between two groups first in left > hemisphere, and got some regions which showed different. > 1) so if I then do multiple correction, i don't need to run the > mri_glmfit-sim command, and just press the button of the monte carlo > null-z simulation in the qdec interface, am i right? correct > 2) Whether mri_glmfit-sim --cache command line and the mc-z in qdec > get the same results, or not? and as to the option --cwpvalthresh, > should i choose 0.05 or 0.025? If you are drawing conclusions from both hemispheres then you need to use .025 > 3) And what is the difference between fdr and mc-z correction? mc-z uses a cluster-wise correction and controls the rate of false positive clusters. FDR is voxel-wise and controls the false discovery rate, which is the number of false positives relative to the total number of positives (as compared to the number of false positives relative to the total number of tests). doug > Thanks, --

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p-val from FDR
by Antonella Kis 18 Jul '12

18 Jul '12

Hi Doug, You mentioned that in my case when FDR found a voxel-wise threshold of 3.8 means p<1.5849e-04. How exactly I you got this p-val? How I can get myp-vals for clusters after FDR? Many thanks. Antonella

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running trac-all -path missing files
by Rui Lavrador 18 Jul '12

18 Jul '12

Hi FS users, I'm running “trac-all –path ” and when running it, it constantly gives the output ERROR: Degenerate spline segment 58 81 24 56 69 24 … But it runs until the end without exiting and says that it ran without errors. It’s normal? Plus, it seems that it fails to create the output files. When looking at the created folder “…/Diff001/dpath” there is only one folder “5cpts”, so I cannot visualize the WM pathways, with freeview, that should be located, for example at “…/dpath/lh.ilf_AS_avg32_mni_flt/path.pd.nii.gz” Any suggestions? -- Rui Lavrador

2 1

Sourcing error?
by jwaugh＠nmr.mgh.harvard.edu 18 Jul '12

18 Jul '12

Hello, I am having difficulty with an fMRI command line program that we have run successfully in the past, but which we haven't used in ~4 months. In response to the following command lines (from a csh script): "setenv FSL_DIR $FSLDIR source /usr/local/freesurfer/nmr-stable3-env source ${FSLDIR}/etc/fslconf/fsl.csh setenv FSLOUTPUTTYPE ANALYZE setenv SUBJECTS_DIR /cluster/ablood/1/R01_Botox cd /cluster/ablood/1/R01_Botox preproc-sess -s CD_R01BTX_CTRL7_sess1 -df sessdirfile -mcout fmc5 -fwhm 5 -smin fmc5 -smout fmcsm5 preproc-sess -s CD_R01BTX_CTRL7_sess1 -df sessdirfile -mcout fmc4 -fwhm 4 -smin fmc4 -smout fmcsm4 mkanalysis-sess.new -analysis tap_lh_long_CD_R01BTX_CTRL7_sess1_sm5 -TR 2.5000 -paradigm 60_60_60_60_60_60_60.para -designtype blocked -funcstem fmcsm5 -motioncor -runlistfile runlistfile_tap_lh_long -inorm -tpef tpexclude60_60_60_60_60_60_60 -nconditions 1 -timewindow 25.0000 -gammafit 2.25 1.25 -s CD_R01BTX_CTRL7_sess1 -df sessdirfile selxavg-sess -analysis tap_lh_long_CD_R01BTX_CTRL7_sess1_sm5 -s CD_R01BTX_CTRL7_sess1 -df sessdirfile mkcontrast-sess -analysis tap_lh_long_CD_R01BTX_CTRL7_sess1_sm5 -contrast tap_lh_long_CD_R01BTX_CTRL7_sess1_sm5_contrast -a 1 -c 0 stxgrinder-sess -analysis tap_lh_long_CD_R01BTX_CTRL7_sess1_sm5 -contrast tap_lh_long_CD_R01BTX_CTRL7_sess1_sm5_contrast -s CD_R01BTX_CTRL7_sess1 -df sessdirfile" we get the following error messages: ERROR: cannot find /usr/pubsw/packages/fsl/current/bin/ip ERROR: ipfsl failed ERROR: spatialsmooth-sess failed In the past such an error has resulted from using the newer source environment (stable-5.1), but would always work when sourced with stable-3. I have re-run this with stable-5.1 as well, but we get the same type of error. Any help would be much appreciated! Thanks, Jeff

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Re: [Freesurfer] FDR versus mri_glmfit-sim with --cache option
by Douglas N Greve 18 Jul '12

18 Jul '12

It should be the sig.mgh file in your contrast directory. doug ps. Please post to the list and not me directly. thanks! On 07/18/2012 11:56 AM, Antonella Kis wrote: > Hi Doug, > > Many thanks for your prompt response and your help. I have one more > question please. I searched for mri_surfcluster command and I am not > sure what should be my input file. > > Can you please clarify this for me? Should this be L-frontal.fsgd > since I have more subjects? > > > Thank you. > Antonella > > ------------------------------------------------------------------------ > *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > *To:* freesurfer(a)nmr.mgh.harvard.edu > *Sent:* Wednesday, July 18, 2012 11:39 AM > *Subject:* Re: [Freesurfer] FDR versus mri_glmfit-sim with --cache option > > Hi Antonella, first of all, FDR and clusterwise correction are doing > different things. Technically, you don't get clusters from FDR. FDR will > choose a voxel-wise threshold for you, and any voxel above threshold can > be interpreted as surviving FDR (but you should know how to interpret it > -- see Tom Nichols' paper). Of course, many of the voxels may appear as > clusters. In your case, FDR found a voxel-wise threshold of 3.8 > (meaning p<1.5849e-04). The fastest way to get the values you want is > to go outside of QDEC. First, run mri_surfcluster using a threshold of > 3.8 (--thmin 3.8). Specify an output cluster number map (--ocn ocn.mgh) > and a summary file (--sum sum.dat). This will produce a lot of > "clusters", two of which should be the ones below (you can prune the > list by specifying that the clusters need to be a certain size > (--minarea). Once you have the ocn file, you can run mri_segstats, > something like > mri_segstats --seg ocn.mgh --i y.mgh --avgwf avgwf.dat --excludeid 0 > y.mgh is the glmfit input file created by qdec. This will produce > avgwf.dat which will have a column for each cluster, the order will be > the same as that in sum.dat. > > douig > > On 07/18/2012 11:25 AM, Antonella Kis wrote: > > Dear FS team, > > > > > > > > I am doing a cortical thickness study using QDEC. I used FDR and got > > the following clusters: > > > > Generating cluster stats using min threshold of 3.8... > > Found 2 clusters > > Contrast: 'lh-Diff-Class1-Class2-Intercept-thickness', 15fwhm, DOF: 69 > > ClusterNo Max VtxMax Size(mm2) TalX TalY TalZ NVtxs Annotation > > --------- --- ------ --------- ---- ---- ---- ----- ---------- > > 1 -3.8743 18231 4.55 -39.8 1.5 14.1 14 precentral > > 2 -3.8065 47386 2.66 -8.2 33.1 33.9 4 > superiorfrontal > > ============================================================ > > I need to get the cortical thickness values from each subject within > > this clusters so I am trying to use > > mri_glmfit-sim with --cache option and I wonder what value should I > > choose in this case for cache (2, 3.3 or 4) > > and what --cwpvalthresh 0.05 or .025 to get the same results as FDR's > > results. > > > > I tried: > > mri_glmfit-sim \ > > --glmdir lh.L_frontal.glmdir \ > > --cache 3 neg \ > > --cwpvalthresh .05 \ > > --overwrite > > > > # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP > > CWPLow CWPHi NVtxs Annot > > 1 -3.874 18231 320.36 -39.8 1.5 14.1 0.02610 > > 0.02410 0.02820 949 precentral > > 2 -3.807 47386 700.61 -8.2 33.1 33.9 0.00020 > > 0.00000 0.00040 1053 superiorfrontal > > > > so as you can see the clusters are the same but their Size and NVtxs > > is so different. What is wrong? > > > > Thank you for your time and help. > > Antonella > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > > 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> > Phone Number: 617-724-2358 > Fax: 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> > > _______________________________________________ > 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. > > > -- 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] ask for help
by Douglas N Greve 18 Jul '12

18 Jul '12

Hi Haochuanxi, what is the context of this question? Are you running a qdec analysis? What are your variables? doug ps. Please post your questions to the freesurfer list instead of me directly. thanks! On 07/18/2012 11:55 AM, 传玺 wrote: > Dear Doulgus > Could you tell me the exactly meaning of "a significant group by > gender interaction was found ", that is, what is the meaning of "group > by gender interaction "? > I know it is not your duty to answer this question, but it is > important to understand that concept to me, so I would be grateful to > you if you lend me a hand! > BEST WISHES! > Haochuanxi > Peking University China > > > 来自网易手机邮箱了解更多 <http://shouji.163.com> -- 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] FDR versus mri_glmfit-sim with --cache option
by Antonella Kis 18 Jul '12

18 Jul '12

Hi Doug, Many thanks for your prompt response and your help. I have one more question please. I searched for mri_surfcluster command and I am not sure what should be my input file. Can you please clarify this for me? Should this be L-frontal.fsgd since I have more subjects? Thank you. Antonella

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Freesurfer July 2012