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Fwd: OHBM 2016 Call For Council Nominations
by Douglas N Greve 05 Oct '15

05 Oct '15

-------- Forwarded Message -------- Subject: OHBM 2016 Call For Council Nominations Date: Mon, 05 Oct 2015 09:59:50 -0500 From: info(a)humanbrainmapping.org Reply-To: info(a)humanbrainmapping.org To: greve(a)nmr.mgh.harvard.edu Dear OHBM Member: Why is strong leadership so important? Does it really matter if an association has strong leaders? Yes, both history and experience suggest that leadership IS very important to the success of an association. Strong leadership is essential to setting and accomplishing OHBM’s strategic goals and in anticipating future needs. The OHBM Nominating Committee will continue to work diligently to develop a slate of candidates for election on the Executive Council, but *we need your participation now in identifying leadership candidates.* The Nominating Committee is pleased to invite current OHBM members to nominate individuals to serve on the OHBM Executive Council. Open positions include Chair-Elect, Secretary-Elect, Treasurer-Elect, Program Chair-Elect and Education Chair-Elect. The term of service begins in June 2016, and each term is for three years. Please make your nominations by completing the *Call for Nominations* <http://www.humanbrainmapping.org/i4a/forms/index.cfm?id=25> form no later than *Monday, November 9^th at* *11:59 PM US CST*. Self-nominations are welcome and encouraged. OHBM recently went through a rigorous and thoughtful strategic planning session and are seeking individuals with proven scientific leadership expertise, strategic thinking and planning skills, strong problem solving skills, results oriented, visionary, strong ethics, have a global perspective and are available to participate and commit time. A knowledge of OHBM activities and consistent attendance at the Annual Meeting is desired. The OHBM By-Laws <http://www.humanbrainmapping.org/i4a/pages/index.cfm?pageid=3292>, Article 5 provides the framework and process for the election of new Council members. *OHBM Nominating Committee:* Tonya White, Secretary Tor Wager, Secretary-Elect Doug Greve, Past Secretary Karl Zilles, Chair Alan Evans, Chair-Elect Karen Berman, Past Chair You must, when making your nominations, specify a position you want the person to fill (Chair Elect, Treasurer Elect, Secretary Elect, Program Chair Elect, Education Chair-Elect). Please check with this person before you make the nomination to be sure they would be interested in serving. Once the final slate is prepared and distributed, members will be able to see a brief bio on each candidate and vote online via the OHBM website. The results of these elections will be announced during the Town Hall Meeting, Wednesday, June 29, 2016, during the OHBM Annual Meeting in Geneva, Switzerland. All candidates identified on the ballot will be informed of the results prior to the Annual Meeting. Councilors are not eligible for re-election for any council position for three years after serving one term. Individuals who are currently ineligible as nominees due to service on Council within the past 3 years are listed below. *Not Eligible Until 2018/2019* * Steve Smith, 2014-2015 Chair * Jia-Hong Gao, 2014-2015 Treasurer * Simon Eickhoff, 2014-2015 Secretary * Pedro Valdes Sosa, 2014-2015 Program Chair *Not Eligible Until 2017/2018* * Susan Bookheimer, 2013-2014 Chair * Julian Doyon, 2013-2014 Treasurer * Thomas Nichols, 2013-2014 Secretary * Peter Bandettini, 2013-2014 Program Chair * Klaas Enno Stephan, 2013-2014 Education Chair We look forward to your involvement in the identification and election of your association’s leadership. Please contact the OHBM Executive Office at info(a)humanbrainmapping.org <mailto:info@humanbrainmapping.org> with any questions. Sincerely, JoAnn Taie Executive Director Organization for Human Brain Mapping (OHBM) *Organization for Human Brain Mapping* 5841 Cedar Lake Road, Suite 204 Minneapolis, MN 55416 USA Phone: 1 952-646-2029 Fax: 1 952-545-6073 www.humanbrainmapping.org <http://www.humanbrainmapping.org> info(a)humanbrainmapping.org <mailto:info@humanbrainmapping.org> To opt out of OHBM emails, contact the OHBM Executive Office at info(a)humanbrainmapping.org <mailto:info@humanbrainmapping.org?subject=Opt%20Out%20of%20Emails>. <http://www.humanbrainmapping.org/i4a/pages/index.cfm?pageID=3662> *Save the Date! June 26-30, 2016* <http://www.humanbrainmapping.org/i4a/pages/index.cfm?pageID=3662> *Current 2015-2016 Council Members <http://www.humanbrainmapping.org/i4a/pages/index.cfm?pageid=3313>*

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Custom parcellation for HCP data
by Simon Baker 05 Oct '15

05 Oct '15

Hi all, We want to create a custom parcellation for use with the connectome project data. However, we have not been able to achieve accurate spatial alignment between the random parcellation volume and the T1w volume. Specifically, there appears to be an "offset," possibly due to a mismatch between the origin of these volumes. In the following we describe the relevant steps of our pipeline. Please suggest any changes that might help to resolve the issue. 1. Create a high-resolution annotation (parcellation) by randomly parcellating the fsaverage surface into N regions of approximately equal volume. 2. Map the annotation from the source subject (fsaverage) to the target subject using mri_surf2surf. mri_surf2surf --srcsubject fsaverage --hemi lh --sval-annot highres.annot --trgsubject ${SUBJECTID} --srcsurfreg sphere.reg --trgsurfreg ${SUBJECTS_DIR}/${SUBJECTID}/MNINonLinear/Native/${SUBJECTID}.L.sphere.native.surf.gii --tval lh.highres.annot [repeat for rh] 3. Obtain vertices and faces data from ${SUBJECTS_DIR}/${SUBJECTID}/MNINonLinear/Native/${SUBJECTID}.L.white.native.surf.gii [repeat for rh] 4. Using the vertices and faces data obtained in step 3 as inputs for the write_surf Matlab function, create the lh.white surface file. [repeat for rh] 5. Obtain thickness data from ${SUBJECTS_DIR}/${SUBJECTID}/MNINonLinear/Native/${SUBJECTID}.L.thickness.native.shape.gii [repeat for rh] 6. Convert the annotation into a volume using mri_label2vol. mri_label2vol --annot lh.highres.annot --temp ${SUBJECTS_DIR}/${SUBJECTID}/T1w/T1w_acpc_dc_restore.nii.gz --identity --proj frac 0 1 .1 --subject ${SUBJECTID} --hemi lh --o vol_lh.nii [repeat for rh] 7. Configure the volume (remove unwanted ROIs). [repeat for rh] 8. Combine the configured volumes from each hemisphere to create the random parcellation volume. 9. Overlay the random parcellation volume on the template volume. See attached screenshot.jpeg showing the misalignment between the random parcellation volume and the template volume. Kind regards, Simon Baker Brain & Mental Health Laboratory Institute of Cognitive & Clinical Neuroscience Monash University

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Re: [Freesurfer] fsaverage error with recon-all
by Douglas Greve 05 Oct '15

05 Oct '15

Try removing -ba_labels (it will do that with -all anyway) On 9/29/15 9:02 PM, 葉丁瑞 wrote: > Dear All, > > I ran the following script: > recon-all -i /Volumes/yang/S002_AD1118_20090116/NCKU-0003-0000-00001.dcm -s S002_ba -sd /Volumes/yang/S002_AD1118_20090116/ -all -ba_labels > and got the error below at the end. Could anybody please let me know how to fix it. > --- > > SUBJECTS_DIR /Volumes/yang/S002_AD1118_20090116 > > FREESURFER_HOME /Applications/freesurfer > > Loading source label. > > No such file or directory > > ERROR reading > /Volumes/yang/S002_AD1118_20090116/fsaverage/label/lh.BA1.label > > Darwin MRI2deiMac.local 13.4.0 Darwin Kernel Version 13.4.0: Wed Mar > 18 16:20:14 PDT 2015; root:xnu-2422.115.14~1/RELEASE_X86_64 x86_64 > > recon-all -s S002 exited with ERRORS at Sat Sep 26 21:57:00 CST 2015 > > For more details, see the log file > /Volumes/yang/S002_AD1118_20090116/S002/scripts/recon-all.log > > To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > --- > > I follow the below step at freesurfer message board > cd /Volume/yang > > ln -s /Applications/freesurfer/subjects/fsaverage > > recon-all -i /Volumes/yang/S002_AD1118_20090116/NCKU-0003-0000-00001.dcm -s S002_ba -sd /Volumes/yang/S002_AD1118_20090116/ -all -ba_labels > but the error is not resoled.please see attached file below > my environment for Freesurfer/FS-FAST > > -------- freesurfer-Darwin-lion-stable-pub-v5.3.0 -------- > > > Setting up environment for FreeSurfer/FS-FAST (and FSL) > > > FREESURFER_HOME /Applications/freesurfer > > > FSFAST_HOME /Applications/freesurfer/fsfast > > > FSF_OUTPUT_FORMAT nii.gz > > > SUBJECTS_DIR /Applications/freesurfer/subjects > > > MNI_DIR /Applications/freesurfer/mni > > > FSL_DIR /usr/local/fsl > > Thank you, > > TING-JUI YEH > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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FSGD for A mixed effect model approach in within subject dataset
by pablo najt 05 Oct '15

05 Oct '15

Hello JorgeTrying to set up for running Linear Mixed Effects. My design has 3 groups (HC, PT relatives and PT) and therefore I am not using QDEC as suggested in the tutorial. My first question: Are there any changes from the matlab commands you suggest in the tutorial if using fsgd rather than Qdec?About my design matrix you suggested below to use each family as the same subject. So I will have family_1 as subject_1, family_2 as subject_2... In my fsgd I need to define at the top the classes and in my matrix these will be the families (family_1, ...). However I also have a number of discrete variables which I define within the classes when running my glm, so I am wondering does this mean that I will be defining my classes as follow?class HC_Female_Family1class PT_Female_Family1class HC_Male_Family2etc Many thanks,Pablo Date: Thu, 10 Sep 2015 13:44:36 +0000 From: jbernal0019(a)yahoo.es To: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] A mixed effect model approach in within subject dataset Hi Pablo I think you can use LME to analyze your data by ordering the rows of your design matrix appropriately. You can consider all subjects belonging to the same family as if they were a single subject in a longitudinal analysis. You can put in your design matrix all subjects belonging to family1 first, then all subjects belonging to family 2 and so on. Then the 'ni' required by lme_mass_fit_vw is a vector with the number of subjects in each family as its entries (ordered according to your design matrix). So the length of the 'ni' vector is equal to the number of different families in your data. Now you can go further and additionally order the rows of your design matrix within each family by age. This will allow you to test the effect of age within family. When choosing the random effects for your statistical model remember that a random effect can only be the intercept term or any covariate that varies within family. For example you can compare a model with a single random effect for the intercept term against the same model but considering both the intercept term and age as random effects. Hope that helps Cheers -Jorge De: pablo najt <pablonajt(a)hotmail.com> Para: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Enviado: Jueves 10 de septiembre de 2015 8:07 Asunto: [Freesurfer] A mixed effect model approach in within subject dataset Dear Freesurfer users,I wanted to enquire if anyone had successfully been able to implement Bernal's Linear Mixed Effects (LME) Models in cross-section dataset *not longitudinal* (please see previous thread below). I am willing to perform a LME (3 groups (HC, PT and Unaffected_relatives) and 3 covariates (sex, age, and family) with "family" variable been a within-subject factor. LME will allow to control for the non-independence of data contributed by patients and relatives from the same families.Thanks in advance!Pablo From: michaelnotter(a)hotmail.com To: freesurfer(a)nmr.mgh.harvard.edu Date: Wed, 19 Feb 2014 13:10:09 +0100 Subject: [Freesurfer] Analysis of structural data acquired from multiple sites by using a mixed effect model approach Hi everybody, I want to compare the surface data of 3 groups (GroupA, GroupB and Controlls) but have the problem that they were acquired from 4 different scanner sites. As I can see it, there are three ways how I could tackle this problem: 1. I could use mri_glmfit and create a qdec table / fsgd-file with 12 classes: Class GroupA_site1; Class GroupA_site2,... And then use the contrasts [0.25 0.25 0.25 0.25 0 0 0 0 -0.25 -0.25 -0.25 -0.25] to compare GroupA to the Controlls. My Problem with this approach is, that the sites don't contribute the same amount of subjects to the analysis. I'm not sure if this could be handled by simply using a weighted contrast. Meaning, if Site1 and Site2 had twice as many subjects than Site3 and Site4, I could modify the contrast to [0.33 0.33 0.17 0.17 0 0 0 0 -0.33 -0.33 -0.17 -0.17]. 2. I could create dummy variables to account for the variability between sites. In this case, I only need to specify 3 classes (Class GroupA; Class GroupB; Class Controlls) in my fsgd-file. And I use a design matrix that has 4 dummy variables at the end, which specify to which site a subject belongs. This approach might work, but I'm not confident that it is the right one. 3. I could use a mixed effect model approach and specify site as a random effect. If I understand it correctly, the mixed effect model approach would be the best one, as it accounts for the variability within sites. Is that correct or are there other issues/better approaches? I tried to implement a mixed effect model by using Bernal's Linear Mixed Effects (LME) Models (http://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels) but run into some problems. I'm not sure if LME can only be applied on longitudinal data or if my implementation is wrong. I have a design matrix X that specifies the characteristics of each subject per row as follows: Intercept GroupA GroupB Controll Age IQ Site1 Site2 Site3 Site4 1 1 0 0 11.1 99 0 0 1 0 1 0 1 0 11.1 101 0 0 1 0 1 1 0 0 11.4 95 1 0 0 0 1 0 0 1 12.4 100 1 0 0 0 ... As I have no repeated measures, 'ni' is just a vector with length X containing '1's. If I do now the vertex-wise linear mixed-effects estimation, I get the following output: >> stats = lme_mass_fit_vw(X,[7 8 9 10],Y,ni,lhcortex); Starting matlabpool using the 'local' profile ... connected to 8 workers. Starting model fitting at each location ... Location 24994: Index exceeds matrix dimensions. Location 24994: Algorithm did not converge. Initial and final likelihoods: -10000000000, -10000000000. Location 62484: Index exceeds matrix dimensions. Location 62484: Algorithm did not converge. Initial and final likelihoods: -10000000000, -10000000000. ... I've checked the matrix dimensions of X, Y, ni and lhcortex and compared them to the LME mass_univariate example stored in ADNI_Long_50sMCI_vs_50cMCI.mat but couldn't find any divergence. Has anybody encountered similar problems? Is my approach of specifying 'ni' as a vector of'1's even legitimate? Thanks, Michael _______________________________________________ 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. _______________________________________________ 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. _______________________________________________ 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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Postdoctoral Fellow in Machine Learning in Neuroimaging
by Thomas Yeo 05 Oct '15

05 Oct '15

Dear All, I am looking to hire a postdoc to develop machine learning algorithms for fMRI. Topics are flexible. Example topics include dynamic functional connectivity, meta-analysis, neural mass modeling, monkey-human homologies, mental disorder subtypes, etc. Other details below. Regards, Thomas Requirements: Ph.D. in computer science, electrical engineering, statistics, computational neuroscience or related fields. The successful applicant will work with an interdisciplinary team of computer scientists and neuroscientists, and must be willing to learn some neuroscience. Research Webpage: https://sites.google.com/site/yeoyeo02/home Compensation: Competitive and commensurate with experience Attraction: Perform ground-breaking research at the National University of Singapore (NUS), while enjoying the beautiful sceneries and cultures of South-East Asia. NUS is a research-intensive university consistently ranked among the top 30 universities in the world (http://en.wikipedia.org/wiki/National_University_of_Singapore#University_ra…) Contact: Email BT Thomas Yeo (ythomas(a)csail.mit.edu) with your CV. Deadline: Whenever the position is filled.

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Tracula: Segmentation fault
by andrea cristina Lima 02 Oct '15

02 Oct '15

Please could you help me with this? Computing prior on underlying anatomy (non-truncated streamlines only) Segmentation fault Darwin macprolim446.local 14.5.0 Darwin Kernel Version 14.5.0: Wed Jul 29 02:26:53 PDT 2015; root:xnu-2782.40.9~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Fri Oct 2 19:38:55 BRT 2015 Attached is the log Thank you! -- Andrea Cristina de Lima Pardini CV: http://lattes.cnpq.br/0921194840474573

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Re: [Freesurfer] PVE correction tool within the V 6 beta
by m.bahri＠ulg.ac.be 02 Oct '15

02 Oct '15

Dear Greve, Thank you for your answer. Steps 1 and 2 are ok but in step 3 there are some unclear options (e.g. --mgx .01) Could you please explain which method is used for the pve correction and how can I obtain the 4D-pve-corrected images? Is it possible to extract the TACS of all regions? Many thanks for your help, Best, Mohamed ----- Mail original ----- De: "Douglas Greve" <greve(a)nmr.mgh.harvard.edu> À: freesurfer(a)nmr.mgh.harvard.edu Envoyé: Lundi 28 Septembre 2015 17:49:49 Objet: Re: [Freesurfer] PVE correction tool within the V 6 beta I'm still putting all the documentation together, but you can start with the instructions below. They are assuming you will use kinetic modeling. If you have a static scan, #1 and #2 are still the same, but #3 changes and #4 and #5 not needed. Let me know and I can give you further instructions. doug 1. To start, run gtmseg --s subject This will take a couple of hours and produces some files needed for GTM PVC (which is used for GTM, MG, RBV). 2. You'd then register the PET to the anatomical with bbregister (with --t2 weighting). Make sure to save the output as an LTA (--lta). I usually use the mean TAC as the input. You can do this in parallel with #1. 3. You'd then run mri_gtmpvc, something like mri_gtmpvc --i tac.nii.gz --psf PSF --auto-mask PSF+2 .01 --seg gtmseg.mgz --reg reg.lta --default-seg-merge --mgx .01 --o gtmpvc.output --km-hb 11 12 13 50 51 52 --km-ref 8 47 --no-rescale PSF is the point-spread FWHM of the scanner; reg.lta is the registration from #2. --km-hb specifies the highbinding region for MRTM2. --km-ref specifies the reference region. --mgx specifies to output a muller-gartner map (not necessary for GTM ROI analysis). 4. For the GTM (ROI) MRTM1 KM analysis, you would then run mri_glmfit --y km.hb.tac.nii.gz --mrtm1 km.ref.tac.dat time.dat --o mrtm1 --no-est-fwhm --nii.gz where time.dat is a text file withe acquisition time of each time point in the tac. 5. For the MRTM2 analysis set k2p = `cat mrtm1/k2prime.dat` mri_glmfit --y km.hb.tac.nii.gz --mrtm2 km.ref.tac.dat time.dat $k2p --o mrtm1 --no-est-fwhm --nii.gz If you want to run a voxel-wise analysis, then you can use the mgx volume as input (--y). Probably you'll want to sample this to the surface using mri_vol2surf and the registration file aux/anat2pet.lta, then smooth on the surface On 9/28/15 11:38 AM, Mohamed Ali Bahri wrote: > Dear Expert, > > Are there any explanation (steps to follow) about the use of FreeSurfer > (version 6 beta) to correct for the partial volume effect (PET dynamic > data)? > > Many thanks in advance, > > Best, > > Mohamed > _______________________________________________ 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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Re: [Freesurfer] warping surface label to volume space
by Douglas N Greve 02 Oct '15

02 Oct '15

I'm at a loss here. I run the exact same command with the same version. I get the same terminal output, but my output volume looks ok. The only thing I can think of is that there is an old version that output volume that is not getting overwritten. Can you name the output file differently and make sure that it does not exist prior to running the command? On 09/30/2015 04:37 PM, Jacobs H (NP) wrote: > Hi Doug, > > Just as a reminder: I uploaded the data yesterday. > > Best > Heidi > > From: Douglas Greve <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > Date: Tuesday 29 September 2015 17:01 > To: "freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>" > <freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > Subject: Re: [Freesurfer] warping surface label to volume space > > filedrop2 url at the end of this email > > On 9/29/15 10:34 AM, Jacobs H (NP) wrote: >> Sure, where should I upload it to? >> Thanks! >> Heidi >> >> From: Douglas Greve <greve(a)nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu>> >> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu >> <mailto:freesurfer@nmr.mgh.harvard.edu>> >> Date: Tuesday 29 September 2015 16:28 >> To: "freesurfer(a)nmr.mgh.harvard.edu >> <mailto:freesurfer@nmr.mgh.harvard.edu>" >> <freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> >> Subject: Re: [Freesurfer] warping surface label to volume space >> >> Can you upload the subject so I can look at it? >> >> On 9/29/15 9:05 AM, Jacobs H (NP) wrote: >>> Hi Doug, >>> >>> The label looks actually ok and the surface as well. I attached the images to this email, Not sure where it went wrong? >>> >>> Best >>> Heidi >>> >>> ________________________________________ >>> Van:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] namens Douglas N Greve [greve(a)nmr.mgh.harvard.edu] >>> Verzonden: maandag 28 september 2015 23:58 >>> Aan:freesurfer@nmr.mgh.harvard.edu >>> Onderwerp: Re: [Freesurfer] warping surface label to volume space >>> >>> Something is definitely going wrong. Can you load the label as well and >>> verify that the label itself looks ok? >>> >>> On 09/28/2015 05:32 PM, Jacobs H (NP) wrote: >>>> Yes, here it is! >>>> Thanks! Heidi >>>> >>>> >>>> >>>> Yes, here it is! >>>> Thanks! Heidi >>>> >>>> >>>> image1.png >>>> >>>> >>>> >>>> ATT00001.txt >>>> >>>> >>>> >>>>> Op 28 sep. 2015 om 17:26 heeft Douglas N Greve<greve(a)nmr.mgh.harvard.edu> het volgende geschreven: >>>>> >>>>> Can you send a picture? >>>>> >>>>>> On 09/28/2015 05:08 PM, Jacobs H (NP) wrote: >>>>>> Dear Doug, >>>>>> >>>>>> By looking at it in Freeview. Anatomically, I would expect that the entorhinal cortex would not be localized so laterally? And some voxels are not in the temporal lobe. >>>>>> >>>>>> Best >>>>>> Heidi >>>>>> >>>>>> ________________________________________ >>>>>> Van:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] namens Douglas N Greve [greve(a)nmr.mgh.harvard.edu] >>>>>> Verzonden: maandag 28 september 2015 23:00 >>>>>> Aan:freesurfer@nmr.mgh.harvard.edu >>>>>> Onderwerp: Re: [Freesurfer] warping surface label to volume space >>>>>> >>>>>> how are you determining that it is not in the right place? When I run >>>>>> this it works. >>>>>> >>>>>>> On 09/28/2015 04:54 PM, Jacobs H (NP) wrote: >>>>>>> Hi, >>>>>>> >>>>>>> Bringing this to the FS list: >>>>>>> I am trying to warp the entorhinal cortex label (ex vivo) to volume >>>>>>> space, so that I can see and use the full ROI. Using the command >>>>>>> stated below doesnâ€™t seem to work, as it is not in the right location >>>>>>> of the subjectâ€™s brain. Any thoughts? >>>>>>> >>>>>>> I used this command: >>>>>>> mri_label2vol --label S_3RSPPP/label/lh.entorhinal_exvivo.label >>>>>>> --regheader $SUBJECTS_DIR/S_3RSPPP/mri/orig.mgz --o >>>>>>> lh.entorhinal_exvivo_vol.mgz --fill-ribbon --subject S_3RSPPP --hemi l >>>>>>> >>>>>>> This was the output on the terminal: >>>>>>> subject S_3RSPPP --hemi lh >>>>>>> INFO: subject not needed, igorning. >>>>>>> Number of labels: 1 >>>>>>> S_3RSPPP/label/lh.entorhinal_exvivo.label >>>>>>> Annot File: (null) >>>>>>> Template Volume: (null) >>>>>>> Outut Volume: lh.entorhinal_exvivo_vol.mgz >>>>>>> Registration File: (null) >>>>>>> Fill Threshold: 0 >>>>>>> Label Vox Vol: 1 >>>>>>> ProjType: (null) >>>>>>> ProjTypeId: 0 >>>>>>> ProjStart: 0 >>>>>>> ProjStop: 0 >>>>>>> ProjDelta: 0.1 >>>>>>> Subject: S_3RSPPP >>>>>>> Hemi: lh >>>>>>> UseNewASeg2Vol: 0 >>>>>>> DoLabelStatVol 0 >>>>>>> LabelCodeOffset 0 >>>>>>> setenv SUBJECTS_DIR /autofs/space/schopenhauer_003/users/hjacobs/SUBJECTS >>>>>>> $Id: mri_label2vol.c,v 1.46 2014/12/08 21:11:54 greve Exp $ >>>>>>> INFO: loading >>>>>>> surface /autofs/space/schopenhauer_003/users/hjacobs/SUBJECTS/S_3RSPPP/surf/lh.white >>>>>>> >>>>>>> nvertices = 120130 >>>>>>> Reading thickness >>>>>>> /autofs/space/schopenhauer_003/users/hjacobs/SUBJECTS/S_3RSPPP/surf/lh.thickness >>>>>>> nlabels = 1 >>>>>>> Loading >>>>>>> /autofs/space/schopenhauer_003/users/hjacobs/SUBJECTS/S_3RSPPP/mri/ribbon.mgz >>>>>>> Loading S_3RSPPP/label/lh.entorhinal_exvivo.label >>>>>>> Mapping >>>>>>> >>>>>>> Any suggestions how I can improve this? >>>>>>> Thanks >>>>>>> Heidi >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Freesurfer mailing list >>>>>>> Freesurfer@nmr.mgh.harvard.eduhttps://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:https://gate.nmr.mgh.harvard.edu/filedrop2www.nmr.mgh.harvard.edu/… >>>>>> Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer@nmr.mgh.harvard.eduhttps://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. >>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer@nmr.mgh.harvard.eduhttps://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:https://gate.nmr.mgh.harvard.edu/filedrop2www.nmr.mgh.harvard.edu/… >>>>> Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.eduhttps://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:https://gate.nmr.mgh.harvard.edu/filedrop2www.nmr.mgh.harvard.edu/… >>> Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] mri_convert doubles file size when changing TR header information
by Douglas Greve 02 Oct '15

02 Oct '15

It is probably changing the data type from short to float. Try adding -odt short --no_scale 1 You can also look at the data type with mri_info --type file.nii On 10/1/15 10:52 AM, Shaun Patel wrote: > I noticed after running slice-time correction with SPM, the resulting Nifti files do not have TR information in the header. This breaks the Freesurfer pipeline. To get around this, I attempted to use the mir_convert function with the “tr” flag to set the TR. However, in doing so, I noticed that the resulting nifti file doubles in size. I used the following command: mri_convert f.nii f.nii -tr 2000, to set the TR to 2s. Any suggestions as to what is happening to the file size and how to prevent it? > > Many Thanks, > > Shaun > > -- > Shaun Patel, Ph.D. > Research Fellow > Department of Neurosurgery > Massachusetts General Hospital > Harvard Medical School > e. shaun.patel(a)me.com > w. http://shaunpatel.com > c. 317.340.7260 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >

1 0

] dt_recon
by Alshikho, Mohamad J. 02 Oct '15

02 Oct '15

Hi Doug, Thank you very much for your answers! Kindly I have one more question: At the end of DTI analysis using the tool “dt_recon” we will have “ stats” file including the FA value for every segment and parcellate in the brain. Depending on this output can we use the term “ DTI morphometry” to describe the analysis? Thanks Mohamad From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve Sent: Monday, September 28, 2015 11:26 AM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] dt_recon On 9/25/15 9:28 AM, Alshikho, Mohamad J. wrote: Hi Doug and Bruce, After running the command : dt_recon --i 6-1025.dcm --s M87102113 --o dti dt_recon --i f.nii --b f.bvals f.bvecs --s M87102113 --o dti <<< source: Freesurfer wiki>>> I need to generate the final statistics ( FA for every parcellate and segment in aseg and wmparc atlases) using the command “mri_segstats” In order to do so I need to move “fa.nii” to anatomical space using the command: mri_vol2vol –mov fa.nii –lta register.lta –fstarg –o fa.anat.mgh <<< source: Freesurfer wiki>>> My questions are about the file “register.lta” : 1. What is the difference between this file and the file “register.dat” ( which I can see it as an output of the command ” bbregister” in the final analysis using the command “dt_recon”) They hold the same basic registration information just in different formats. We are trying to move to the LTA as it is a much better format for these things. 2. How can I generate the file “ register.lta”? Use lta_convert, something like lta_convert --inreg register.dat --outlta register.lta --src lowb.nii.gz --trg $SUBJECTS_DIR/$subject/mri/orig.mgz 3. Can I feed the file “ register.dat” instead of the file “ register.lta” into the command “mri_vol2vol “ (in order to move the ‘’fa.nii” to anatomical space). If so which flag I should use instead of the flag “--lta” in the command mri_vol2vol? Yes, pass it with --reg flag. Many thanks Mohamad _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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