Freesurfer March 2012

freesurfer@nmr.mgh.harvard.edu

137 participants
209 discussions

fsaverage
by Ahmed, F, Me <fahmed＠sun.ac.za> 29 Mar '12

29 Mar '12

Hello, I'm trying to run qdec on my own data and I'm trying to create fsaverage. Following the wiki tutorial, I copied the command: if (! -e fsaverage) ln -s $FREESURFER_HOME/subjects/fsaverage but I got the following error: bash: syntax error near unexpected token `ln' Can anyone help me in understanding why this happened? Thanks very much, Fatima ________________________________ E-pos vrywaringsklousule Hierdie e-pos mag vertroulike inligting bevat en mag regtens geprivilegeerd wees en is slegs bedoel vir die persoon aan wie dit geadresseer is. Indien u nie die bedoelde ontvanger is nie, word u hiermee in kennis gestel dat u hierdie dokument geensins mag gebruik, versprei of kopieer nie. Stel ook asseblief die sender onmiddellik per telefoon in kennis en vee die e-pos uit. Die Universiteit aanvaar nie aanspreeklikheid vir enige skade, verlies of uitgawe wat voortspruit uit hierdie e-pos en/of die oopmaak van enige l?ers aangeheg by hierdie e-pos nie. E-mail disclaimer This e-mail may contain confidential information and may be legally privileged and is intended only for the person to whom it is addressed. If you are not the intended recipient, you are notified that you may not use, distribute or copy this document in any manner whatsoever. Kindly also notify the sender immediately by telephone, and delete the e-mail. The University does not accept liability for any damage, loss or expense arising from this e-mail and/or accessing any files attached to this e-mail.

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[FREESURFER] atlas applicability.
by Cheol Han 29 Mar '12

29 Mar '12

Hello freesurfers I am using freesurfer for patients with various neural disease. I wonder the the freesurfer atlas is applicable to them: dementia (with Lewy bodies, DLB), epilepsy, schizophrenia, ADHD, Alzheimer, stroke. (I know some studies already used freesurfer for some of the diseases in the list,) I believe epilepsy patients with lobectomy cannot be applicable. Also is there age limit for the freesurfer atlas? How young can the atlas work for? 4 year-old? 6 year-old? or more than 10 year-old? How about the upper bound? 80 year-old? Thanks for reading and your time! Best Cheol Cheol Han, Ph.D Computational Neuroscience and Neuroinformatics Department of Brain and Cognitive Sciences Seoul National University Korea

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V1_average missing lh.white rh.white
by dgw 28 Mar '12

28 Mar '12

Hello, I am using FreeSurfer 5.1.0. When running recon-all -label_v1 -s $SUBJECT It could not find the rh.white and lh.white surfaces. Subsequently, there was no data in the rh.v1.predict.label. % tksurfer.bin: no data in label file /cluster/haru/uni/1/users/nap_study/struct/nap_01/label/rh.v1.predict.label Additionally, no <subjid>/label/?h.v1.prob.label was created. I am using the V1_average found on the NMR servers (see output of ls -l below run in $SUBJECTS_DIR): V1_average -> /usr/local/freesurfer/stable5_1_0/subjects/V1_average Am I using the wrong V1_average? Do I need to provide any further details? Thanks, Dan Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-v5.1.0-20110514 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-v5.1.0-20110514 INFO: SUBJECTS_DIR is /autofs/cluster/haru/uni/1/users/nap_study/struct Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos4.0_x86_64/stable5_1_0 -rw-rw-r-- 1 dwakeman pls 385906 Mar 28 16:00 /autofs/cluster/haru/uni/1/users/nap_study/struct/nap_01/scripts/recon-all.log Linux gobo 2.6.18-238.9.1.el5 #1 SMP Tue Apr 12 18:10:13 EDT 2011 x86_64 x86_64 x86_64 GNU/Linux #----------------------------------------- #@# Label V1 lh Wed Mar 28 17:05:43 EDT 2012 /autofs/cluster/haru/uni/1/users/nap_study/struct/nap_01/label predict_v1.sh -h lh nap_01 /autofs/cluster/haru/uni/1/users/nap_study/struct/nap_01/surf/lh.inflated.H already exists, skipping. mris_register -inflated -a 4096 -dist 10.0 -parea 1.0 /autofs/cluster/haru/uni/1/users/nap_study/struct/nap_01/surf/lh.sphere /autofs/cluster/haru/uni/1/users/nap_study/struct/V1_average/label/lh.v1.invivo.tif /autofs/cluster/haru/uni/1/users/nap_study/struct/nap_01/surf/lh.v1.invivo.reg using inflated surface for initial alignment using n_averages = 4096 l_dist = 10.000 using l_parea = 1.000 $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading surface from /autofs/cluster/haru/uni/1/users/nap_study/struct/nap_01/surf/lh.sphere... reading template parameterization from /autofs/cluster/haru/uni/1/users/nap_study/struct/V1_average/label/lh.v1.invivo.tif... curvature mean = 0.000, std = 1.000 curvature mean = 0.018, std = 0.041 curvature mean = 0.006, std = 0.891 curvature mean = 0.018, std = 0.043 curvature mean = 0.002, std = 0.959 curvature mean = 0.018, std = 0.045 curvature mean = 0.001, std = 0.981 curvature mean = 0.018, std = 0.049 curvature mean = 0.000, std = 0.991 writing registered surface to /autofs/cluster/haru/uni/1/users/nap_study/struct/nap_01/surf/lh.v1.invivo.reg... curvature mean = 0.000, std = 0.604 curvature mean = 0.004, std = 0.952 curvature mean = 0.037, std = 0.807 curvature mean = -0.011, std = 0.957 curvature mean = 0.012, std = 0.930 curvature mean = -0.020, std = 0.961 curvature mean = 0.006, std = 0.967 curvature mean = -0.024, std = 0.961 curvature mean = 0.002, std = 0.985 curvature mean = -0.026, std = 0.286 curvature mean = 0.002, std = 0.068 curvature mean = 0.065, std = 0.336 curvature mean = 0.002, std = 0.081 curvature mean = 0.039, std = 0.522 curvature mean = 0.002, std = 0.087 curvature mean = 0.019, std = 0.665 curvature mean = 0.002, std = 0.090 curvature mean = 0.007, std = 0.771 expanding nbhd size to 1 mris_spherical_average -osurf v1.invivo.reg -n -o nap_01 label lh.v1.invivo.label lh v1.invivo.reg V1_average /autofs/cluster/haru/uni/1/users/nap_study/struct/nap_01/label/lh.v1.prob.label output surface = v1.invivo.reg painting output onto subject nap_01. processing subject V1_average... MRISreadVertexPosition(white): could not open file /autofs/cluster/haru/uni/1/users/nap_study/struct/V1_average/surf/lh.white No such file or directory MRISreadOriginalProperties: could not read surface file white No such file or directory could not read surface positions from white No such file or directory threshold_labelfile_at_0p8 /autofs/cluster/haru/uni/1/users/nap_study/struct/nap_01/label/lh.v1.prob.label /autofs/cluster/haru/uni/1/users/nap_study/struct/nap_01/label/lh.v1.predict.label thresholding the label...cat: /autofs/cluster/haru/uni/1/users/nap_study/struct/nap_01/label/lh.v1.prob.label: No such file or directory done #----------------------------------------- #@# Label V1 rh Wed Mar 28 18:47:58 EDT 2012 /autofs/cluster/haru/uni/1/users/nap_study/struct/nap_01/label predict_v1.sh -h rh nap_01 /autofs/cluster/haru/uni/1/users/nap_study/struct/nap_01/surf/rh.inflated.H already exists, skipping. mris_register -inflated -a 4096 -dist 10.0 -parea 0.4 /autofs/cluster/haru/uni/1/users/nap_study/struct/nap_01/surf/rh.sphere /autofs/cluster/haru/uni/1/users/nap_study/struct/V1_average/label/rh.v1.invivo.tif /autofs/cluster/haru/uni/1/users/nap_study/struct/nap_01/surf/rh.v1.invivo.reg using inflated surface for initial alignment using n_averages = 4096 l_dist = 10.000 using l_parea = 0.400 $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading surface from /autofs/cluster/haru/uni/1/users/nap_study/struct/nap_01/surf/rh.sphere... reading template parameterization from /autofs/cluster/haru/uni/1/users/nap_study/struct/V1_average/label/rh.v1.invivo.tif... curvature mean = -0.000, std = 1.000 curvature mean = 0.014, std = 0.039 curvature mean = 0.007, std = 0.894 curvature mean = 0.015, std = 0.037 curvature mean = 0.003, std = 0.935 curvature mean = 0.015, std = 0.039 curvature mean = 0.001, std = 0.966 curvature mean = 0.015, std = 0.042 curvature mean = 0.000, std = 0.984 writing registered surface to /autofs/cluster/haru/uni/1/users/nap_study/struct/nap_01/surf/rh.v1.invivo.reg... curvature mean = 0.000, std = 0.598 curvature mean = -0.003, std = 0.935 curvature mean = 0.032, std = 0.805 curvature mean = -0.004, std = 0.942 curvature mean = 0.012, std = 0.925 curvature mean = -0.008, std = 0.944 curvature mean = 0.005, std = 0.965 curvature mean = -0.010, std = 0.943 curvature mean = 0.001, std = 0.984 curvature mean = -0.027, std = 0.279 curvature mean = 0.004, std = 0.070 curvature mean = 0.065, std = 0.345 curvature mean = 0.004, std = 0.084 curvature mean = 0.041, std = 0.531 curvature mean = 0.004, std = 0.090 curvature mean = 0.021, std = 0.675 curvature mean = 0.004, std = 0.093 curvature mean = 0.006, std = 0.787 mris_spherical_average -osurf v1.invivo.reg -n -o nap_01 label rh.v1.invivo.label rh v1.invivo.reg V1_average /autofs/cluster/haru/uni/1/users/nap_study/struct/nap_01/label/rh.v1.prob.label output surface = v1.invivo.reg painting output onto subject nap_01. processing subject V1_average... MRISreadVertexPosition(white): could not open file /autofs/cluster/haru/uni/1/users/nap_study/struct/V1_average/surf/rh.white No such file or directory MRISreadOriginalProperties: could not read surface file white No such file or directory could not read surface positions from white No such file or directory threshold_labelfile_at_0p8 /autofs/cluster/haru/uni/1/users/nap_study/struct/nap_01/label/rh.v1.prob.label /autofs/cluster/haru/uni/1/users/nap_study/struct/nap_01/label/rh.v1.predict.label thresholding the label...cat: /autofs/cluster/haru/uni/1/users/nap_study/struct/nap_01/label/rh.v1.prob.label: No such file or directory done #------------------------------------------ recon-all -s nap_01 finished without error at Wed Mar 28 20:28:12 EDT 2012 done

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Re: [Freesurfer] dt_recon and tractography
by Antonella Kis 28 Mar '12

28 Mar '12

Hi Anastasia, Many thanks for your reply and help. I was wondering that instead to redo all the preprocessing and registration steps s mentioned on FSTutorial/Running Tracula: * Eddy-current correction * Intra-subject registration (diffusion data to T1) * Inter-subject registration (individual subject to a common space) * Creation of cortical and white-matter masks from FreeSurfer recons I can use all this results from my DTI Data Analysis Preprocessing Stream as mentioned on the FSTutorial/Diffusion, by runningfirst the dt_recon (this is performing an Eddy-current correction) and then I resampled structural data in the Diffusion space (aparc+aseg2diff.mgz, wm2diff.mgz), then I applyed the mask to the diffusion data and removed the unwanted "noise", using the 'mri_mask' command to get the masked fractional anisotropy volume (fa-masked.mgz), adc-masked.mgz and then doing individual subject registration on the CVA space and get resampled int CVS space (fa-masked.ANAT+CVS-to-avg35.mgz) using the using mri_cvs_register. I also have all the outputs mentioned under FSL's dtifit since I got them by running dt_recon. So I wonder if is possible to perform a DTI probabilistic tractography using TRACULA by starting only from the last two steps mentioned in trac-all -prep: * Computing anatomical priors for WM pathways, Recontructing WM Pathways, then visualizing the WM pathways, and then doing only statistics. This is what I meant by my previous results. Thank you for your time and help. Antonella ________________________________ From: Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> To: Antonella Kis <atorok9(a)yahoo.com> Cc: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Sent: Wednesday, March 28, 2012 2:07 PM Subject: Re: [Freesurfer] dt_recon and tractography Trackvis does deterministic tractography, not probabilistic. Which previous results do you want to use and why? On Wed, 28 Mar 2012, Antonella Kis wrote: > Dear FS experts, > > I would like to know if for a Diffusion tensor imaging (DTI) tractography study > with TRACULA I can use my previous results from FSTutorial/Diffusion more > exactly my results after running dt_recon and registrations on the CVS space. > If not can you please advise me if for a DTI probabilistic tractography using > my previous results as mentioned above I can use TracVis. > > > Thank you. > Antonella > > > > _______________________________________________ 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.

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dt_recon and tractography
by Antonella Kis 28 Mar '12

28 Mar '12

Dear FS experts, I would like to know if for a Diffusion tensor imaging (DTI) tractography study with TRACULA I can use my previous results from FSTutorial/Diffusion more exactly my results after running dt_recon and registrations on the CVS space. If not can you please advise me if for a DTI probabilistic tractography using my previous results as mentioned above I can use TracVis. Thank you. Antonella

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Skull strip
by Vincent 28 Mar '12

28 Mar '12

Hi, I have an image that is completing the skull strip with a lot of skull/dura remaining and it is affecting the surfaces. I've tried lowering the watershed threshold as low as 5 and I've tried adding the -gcut option, but the low threshold by itself does not eliminate the skull and gcut not only fails to remove the dura affecting my surfaces but it removes cerebellum as well. There is enough skull/dura left that I am hesitant to try manual edits, but I don't know any other options. I believe a good source of my trouble comes from my own confusion about how much remaining dura/skull is acceptable and how much cerebellum can be missing without affecting the rest of the data. I've uploaded the file (AL.zip) to the FTP server. If anybody has the time I would greatly appreciate it if I could have it looked at. Thank you very much. --Vincent

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(no subject)
by Antonella Kis 28 Mar '12

28 Mar '12

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Re: [Freesurfer] volume mapping
by Douglas N Greve 28 Mar '12

28 Mar '12

And what coordinate system are the xyz in? doug ps. Please post questions to the list and not to me personally. Thanks! On 03/27/2012 04:10 PM, Johnson wrote: > Hi > I have the tracts in (x,y,z) format not as an nii file > regards > JG > On 03/27/2012 11:25 AM, Douglas N Greve wrote: >> Hi Johnson, try something like this: >> >> mri_label2vol --seg tracts.nii --temp orig.mgz --o tracts-in-fs.nii >> --regheader tracts.nii >> >> doug >> >> >> On 03/26/2012 03:29 PM, Johnson wrote: >>> OK >>> T1 space is the space acquired from the machine, original anatomical >>> space >>> regards >>> JG >>> >>> On 03/26/2012 2:25 PM, Bruce Fischl wrote: >>>> can you post to the list so others can answer? And can you clarify >>>> what you mean by "T1" space? >>>> >>>> On Mon, 26 Mar 2012, Johnson wrote: >>>> >>>>> Hi >>>>> well, I had to transfer the fiber tracts coordinates from DWI space >>>>> to T1 space, I used the b0 and the T1 for the registration process, I >>>>> got the transformation matrix and applied it onto the tracts and they >>>>> fit very well. >>>>> Now I want to transform the tracts from T1 space to the freesurfer >>>>> space, I need to know the transformation matrix that was used during >>>>> the processing if it was saved in any of the logs >>>>> thanks >>>>> Johnson >>>>> On 03/26/2012 2:09 PM, Bruce Fischl wrote: >>>>>> Hi Johnson >>>>>> >>>>>> what T1 did you register to? Most of the ones we generate (T1.mgz, >>>>>> brainmask.mgz, ...) are in a common coordinate system and you >>>>>> shouldn't >>>>>> have to transform from one to another. >>>>>> cheers >>>>>> Bruce >>>>>> >>>>>> >>>>>> On Mon, 26 Mar 2012, Johnson wrote: >>>>>> >>>>>>> Hi >>>>>>> Let me re-phrase my question: >>>>>>> I already did registration from DWI to T1, this step is OK. >>>>>>> Now I want to go from T1 to FreeSurfer space (aparc+aseg.mgz >>>>>>> file not >>>>>>> the aparc+aseg-in-rawavg file). I know I have two choices: >>>>>>> 1) do registration using bbregister >>>>>>> 2) since Freesurfer during processing have already done this >>>>>>> step, the >>>>>>> transformation matrix is there somewhere, the question is where to >>>>>>> find >>>>>>> it? which log or which file? this choice is better since it is more >>>>>>> accurate. >>>>>>> >>>>>>> Thanks >>>>>>> JG >>>>>>> >>>>>>> On 03/26/2012 12:41 PM, Anastasia Yendiki wrote: >>>>>>>> If you want to register your DWI to T1, you should register to >>>>>>>> mri/brain.mgz. You can do this with bbregister, or with any affine >>>>>>>> registration tool of your choice. >>>>>>>> >>>>>>>> On Mon, 26 Mar 2012, Johnson wrote: >>>>>>>> >>>>>>>>> Hi >>>>>>>>> I found it in a 256x256x256 space while the T1 we use is in >>>>>>>>> different >>>>>>>>> space, I found this page on the registration step: >>>>>>>>> http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat >>>>>>>>> I wish to know how this script work? >>>>>>>>> >>>>>>>>> mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o >>>>>>>>> aseg-in-rawavg.mgz >>>>>>>>> --regheader aseg.mgz >>>>>>>>> >>>>>>>>> what is the transformation used ? >>>>>>>>> JG >>>>>>>>> >>>>>>>>> >>>>>>>>> On 03/26/2012 12:24 PM, Anastasia Yendiki wrote: >>>>>>>>>> Hi Johnson - The aparc+aseg.mgz is in the same space as >>>>>>>>>> the T1 >>>>>>>>>> used as >>>>>>>>>> input to freesurfer. >>>>>>>>>> >>>>>>>>>> a.y >>>>>>>>>> >>>>>>>>>> On Mon, 26 Mar 2012, Johnson wrote: >>>>>>>>>> >>>>>>>>>>> Hi FS expert >>>>>>>>>>> I need to know the transformation matrix itself since I >>>>>>>>>>> will do >>>>>>>>>> the> transformation in matlab. >>>>>>>>>>> I successfully transformed white matter fibers >>>>>>>>>>> coordinates to T1 >>>>>>>>>> using> AIR 5.0 from LONI lab. >>>>>>>>>>> They provide a transformation matrix. >>>>>>>>>>> Now I want to transform the coordinates from T1 to >>>>>>>>>>> Freesurfer >>>>>>>>>> space, so >>>>>>>>>>> my question is: what is the transformation matrix that >>>>>>>>>>> relates >>>>>>>>>> the T1 >>>>>>>>>>> which FS have used for parcellation and segmentation >>>>>>>>>>> with the> >>>>>>>>>> aparc+aseg.mgz file? >>>>>>>>>>> I searched the logs but couldn't find such matrix. >>>>>>>>>>> I don't want to do a registration step since it will be >>>>>>>>>>> less >>>>>>>>>> accurate> than the one that was generated during the >>>>>>>>>> segmentation >>>>>>>>>> process. >>>>>>>>>>> Also is it just one transformation or a combination of >>>>>>>>>> transformations? >>>>>>>>>>>> thanks >>>>>>>>>>>> >>>>>>>>>> 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. >>>>>>>>>> >>>>>> _______________________________________________ >>>>>> 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 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] conjunction analysis in FS
by Douglas N Greve 28 Mar '12

28 Mar '12

Add " --cwsig cwsig.mgh", then load cwsig.mgh as an overlay in tksurfer. Set the threshold to 1.3 (cluster p < .05). doug On 03/28/2012 07:48 AM, Tetiana Dadakova wrote: > Hello Doug, > > I cancel my first question, I realized CWP values are in the same file. > > Regarding second question, my cluster is quite big, so it goes beyond > just one atlas region. I would like to see what regions it cover, but > for this I need to overlay atlas at the surface (desirably the same as > I overlay cluster) in tksurfer. Can I somehow do it? > > Thank you for your time, > Tanja. > > On Tue, Mar 27, 2012 at 9:55 AM, Tetiana Dadakova<tetiana.d(a)gmail.com> wrote: >> Hello Doug, >> >> thank you so much for your reply. >> >> Could you please answer two more questions: >> >> I used the following line >> mri_surfcluster --in conjunction_sig.mgh --thmin 1.3 --thmax 5 --sign >> abs --subject fsaverage --hemi lh --annot aparc --minarea 0 --csd >> /Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm10/abs/th13/mc-z.csd >> --cwsig summary_sig.mgh --sum summary_sig.txt >> >> I get a table summary_sig.txt with all the clusters uncorrected for >> multiple comparisons. Also, I get the corrected clusters >> summary_sig.mgh, which I can visualize with tksurfer. >> >> My questions are: >> 1) Can I get a txt file with corrected (for multiple comparisons) clusters? >> 2) Can I overlay a Desikan-Killiany Atlas in tksurfer? >> >> Thank you again for your help. >> Tanja. >> >> On Mon, Mar 26, 2012 at 8:38 PM, Douglas N Greve >> <greve(a)nmr.mgh.harvard.edu> wrote: >>> You can view it with tksurfer (instead of qdec). You can run the clustering >>> program (mri_surfcluster) to determine the location, max value, and >>> cluster-wise significance. You can run mri_surfcluster with --help to get >>> details, but you'll need to run it something like: >>> >>> mri_surfcluster --in conjunction_sig.mgh --thmin 2 --sign abs --subject >>> fsaverage --hemi lh --annot aparc --csd path/to/csdfile --sum sum.dat >>> >>> where --thmin 2 means to use p<.01 as the voxel-wise cluster-forming >>> threshold, --sign abs means to consider pos or negative values when forming >>> the threshold, sum.dat is the output. The tricky part will be to get the >>> right CSD file. The path will be something like >>> >>> $FREESURFER_HOME/average/mult-comp-cor/fsaverage/lh/cortex/fwhm12/abs/th20/mc-z.cdf >>> >>> where "th20" corresponds to "--thmin 2", and "abs" corresponds to "--sign >>> abs" and "fwhm12" means that the fwhm.dat file in the qdec output directory >>> has a value between 11 and 12. >>> >>> doug >>> >>> >>> >>> On 03/21/2012 11:00 AM, Tetiana Dadakova wrote: >>>> Thank you, Doug, for your explanation about conjunction analysis in >>>> FreeSurfer. >>>> >>>> I did everything as you said using sig maps, and now I have a >>>> conjunction_sig.mgh, which I don't know how to look at. >>>> Is it possible to load it in qdec (my purpose is to see where the >>>> conjunction clusters are located and what is their size, max value, >>>> significance)? >>>> >>>> Best wishes, >>>> Tanja >>>> >>>> On Mon, Aug 29, 2011 at 7:01 PM, Douglas N Greve >>>> <greve(a)nmr.mgh.harvard.edu> wrote: >>>>> For #1, Donald is right about FS -- you have to exclude the subject. For >>>>> #2, >>>>> you can use mri_concat with the --conjunct option (using sig or t or z >>>>> maps >>>>> as input). >>>>> >>>>> the Conjunction option takes the min of the abs across frames >>>>> at each voxel. The output value at the voxel is the min, >>>>> including the true sign of the min. Eg, if the two frames are: >>>>> +2.1 and +3.4 --> +2.1 >>>>> -2.1 and -3.4 --> -2.1 >>>>> +2.1 and -3.4 --> +2.1 >>>>> -2.1 and +3.4 --> -2.1 >>>>> See: Nichols, Brett,Andersson, Wager, and Poline >>>>> NeuroImage, Volume 25, Issue 3, 15 April 2005, 653-660. >>>>> >>>>> doug >>>>> >>>>> >>>>> MCLAREN, Donald wrote: >>>>>> See inline responses.On Wed, Aug 24, 2011 at 7:35 AM, Tetiana Dadakova >>>>>> <tetiana.d(a)gmail.com<mailto:tetiana.d@gmail.com>> wrote: >>>>>> >>>>>> Dear FS experts, >>>>>> >>>>>> I have two questions: >>>>>> >>>>>> 1. In qdec.table.dat file I am specifying several continuous factors, >>>>>> e.g factor1 and factor2. For some subjects factor2 is missing, >>>>>> therefore I leave empty space in those cells. When I load a >>>>>> qdec.table.dat into qdec, the whole line of the subject with missing >>>>>> factor2 is omitted. >>>>>> I was wondering if I can make some input into the empty cell, so that >>>>>> qdec recognizes that for this subject the value is missing only for >>>>>> factor2, and the value for factor1 is present. >>>>>> >>>>>> >>>>>> I'm not sure about Freesurfer, but in all my work with neuroimaging data >>>>>> across platforms, missing data in X requires that the subject to be >>>>>> excluded. The reason is the Y=X1*B+X2*B. Since you don't know X2, you >>>>>> can't >>>>>> find predicted Y and thus you can't find the error associated with that >>>>>> subject. Programs that all allow you to keep the subject often impute >>>>>> the >>>>>> value of the missing data to get the full X matrix or do not use the >>>>>> General >>>>>> Linear Model to find the solution. The GLM approach inverts the X matrix >>>>>> and >>>>>> you can't invert a matrix with an empty cell, as far as I know. >>>>>> >>>>>> >>>>>> 2. Is it possible to do conjunction analysis in FreeSurfer, I mean >>>>>> looking at common differences in two groups as compared to the third >>>>>> group? >>>>>> >>>>>> >>>>>> When I do conjunctions, I use a logical AND. There are other ways, but >>>>>> there are statistical issues. The logical AND will show where group A> >>>>>> group C and where group B> group C. >>>>>> To do this, I load the thresholded surfaces into matlab, make them both >>>>>> binary, multiply one of them by 2, then add the two datasets together. >>>>>> Then >>>>>> write the data back out to the surface. The new values will be 0 for no >>>>>> difference in either group, 1 or 2 for a difference in one of the group >>>>>> comparison, 3 where both groups are different from the third. >>>>>> >>>>>> >>>>>> >>>>>> Thank you for your time and help, >>>>>> Tanja. >>>>>> _______________________________________________ >>>>>> 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. >>>>>> >>>>>> >>>>>> Best Regards, Donald McLaren >>>>>> ================= >>>>>> D.G. McLaren, Ph.D. >>>>>> Postdoctoral Research Fellow, GRECC, Bedford VA >>>>>> Research Fellow, Department of Neurology, Massachusetts General Hospital >>>>>> and >>>>>> Harvard Medical School >>>>>> Office: (773) 406-2464 >>>>>> ===================== >>>>>> This e-mail contains CONFIDENTIAL INFORMATION which may contain >>>>>> PROTECTED >>>>>> HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is >>>>>> intended only for the use of the individual or entity named above. If >>>>>> the >>>>>> reader of the e-mail is not the intended recipient or the employee or >>>>>> agent >>>>>> responsible for delivering it to the intended recipient, you are hereby >>>>>> notified that you are in possession of confidential and privileged >>>>>> information. Any unauthorized use, disclosure, copying or the taking of >>>>>> any >>>>>> action in reliance on the contents of this information is strictly >>>>>> prohibited and may be unlawful. If you have received this e-mail >>>>>> unintentionally, please immediately notify the sender via telephone at >>>>>> (773) >>>>>> 406-2464 or email. >>>>>> ------------------------------------------------------------------------ >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> 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 >>>>> 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 >>>>> >>> -- >>> 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 >>> > -- 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] Failure to convert DICOM files
by Ed Gronenschild 28 Mar '12

28 Mar '12

Hi Doug, These are Siemens DICOMs and I really don't know what happened to these T1 files, we just got them in this format. Only one out of 32 datasets went wrong, so I consider it as an incident. The workaround with dcm2nii worked fine. Nevertheless, if you are interested I can upload the dataset. Ed On 28 Mar 2012, at 15:47, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > Message: 2 > Date: Tue, 27 Mar 2012 12:14:11 -0400 > From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Failure to convert DICOM files > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <4F71E753.3040504(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Is it a siemens dicom? If so, what happened to the ascii header? > Did you > do something to the file? What are the contents of the image? Eg, a > T1? > doug > > On 03/27/2012 05:35 AM, Ed Gronenschild wrote: >> Hi, >> >> I got an error during the first step in recon-all (Mac OS 10.6.8, >> FreeSurfer v5.1.0). The eror message in the log file is: >> >> WARNING: file ...../MR. >> 1.3.12.2.1107.5.2.18.41016.201008031106017688438785.dcm does not >> contain a Siemens ASCII header >> has this file been anonymized? >> ERROR: cannot unpack mosiacs without ASCII header. >> >> This is strange because it is no mosaic file and all the files can >> be converted >> without any problems with e.g., dcm2nii and viewed with OSIRIX. >> >> Cheers, >> Ed >> >> >> >> >> _______________________________________________ >> 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 > 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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Freesurfer March 2012