Freesurfer December 2011

freesurfer@nmr.mgh.harvard.edu

98 participants
157 discussions

Extracting area.pial stats
by Robustelli, Briana (NIH/NIMH) [F] 15 Dec '11

15 Dec '11

Dear FreeSurfer team, I have been looking at area.pial differences in two groups using qdec. I would now like to extract stats for each subject at the gyral level (using the Desikan parcellation). I used aparcstats2table with the measure flag set to area. But these numbers seem off. Is this the correct area or am I somehow getting white matter area and it so how do I get the area of the pial surface? Thank you! Briana Robustelli -- Briana Robustelli Post-Baccalaureate IRTA Laboratory of Brain and Cognition, NIMH/NIH/DHHS Building 10, Room 4C103 10 Center Dr MSC 1366 Bethesda, MD 20892 Phone: (301) 435-4491 Briana.Robustelli(a)nih.gov

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Re: [Freesurfer] multiple overlay - tksurfer
by Douglas N Greve 15 Dec '11

15 Dec '11

Have you tried to change the threshold to see if you see more colors? Don't load it as a segmentation, just look at the overlay. doug vin . wrote: > Thank you so much Doug, > > you are right, it doesn't match exactly, however there is some match. > so, now I am running recon-all T1_1mmMNI.nii, probably it will improve > the registration. > > -extend to previous email - > just to check, I also summed, all binary files. (attached > sum_binarymap.tif : output from tksurfer) > >tksurfer Sub_ID lh inflated -ov sum_binmap.nii -overlay-reg > register.dat -fthresh 0.01 -fmid 0.3 -fslope 1 > > here sum_binmap : > >mri_binarize --i N.nii --min 0.1 --binval N --o Nb.nii > >fscalc 1b.nii add 2b.nii add 3b.nii ... -o sum_binmap.nii > >mris_seg2annot --seg sum_binmap.nii --hemi lh --s vin --o > lh.seg.annot --ctab vin_colortable.txt > > I just wonder, why I only see one color in sum_binmap overlay. > > > > On Wed, Dec 14, 2011 at 6:01 AM, Douglas Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > The fsaverage surface does not intersect very well with the MNI > brain (the problem is that the average surface does not have as > deep folds as an individual). You can see what is going on if you > convert your label to fsaverage space with > > tkmedit fsaverage orig.mgz -surfs -fmin 0.5 -overlay 1.nii > -overlay-reg register.dat > > This will show you the surfaces and the label. If the label does > not intersect the surfaces, at all, then there's not much you can > do. If there is some intersection, then you can run mri_vol2surf > with --projfrac-max -.1 1.1 .1 > > doug > > > > On 12/13/11 10:53 PM, vin . wrote: >> #Registration >> >tkregister2 --mov $d/T1.nii.gz --targ >> $d/mri/brain.mgz \ >> --regheader --reg $d/vin_register.dat --noedit >> >> I have cortical-clusters in 1mm MNI space so, I took 1mm MNI >> brain and registered this on the "fsaverage" default subject's >> /mri/brain.mgz" >> >> Find attached register.dat >> >> #checking registration >> > >> tkregister2 --targ $d/mri/brain.mgz \ >> --mov T1.nii.gz --reg vin_register.dat >> >> find attached register.tiff >> >> Regards, >> vin >> >> >> On Wed, Dec 14, 2011 at 4:40 AM, Douglas Greve >> <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: >> >> Is your register.dat correct? >> >> >> On 12/13/11 10:33 PM, vin . wrote: >>> Thanx Doug, >>> >>> atleast I see, now something. (see attached "seg.mgh -annot >>> seg.annot.tiff) >>> > tksurfer Sub_ID lh inflated -annot seg.annot -ov >>> lh.seg.mgh -fthresh 0.01 -fmid 0.3 -fslope 1 >>> >>> just to check, I also summed, all binary files. (attached >>> sum_binarymap) >>> >tksurfer Sub_ID lh inflated -ov sum_binmap.nii >>> -overlay-reg register.dat -fthresh 0.01 -fmid 0.3 -fslope 1 >>> >>> also find colortable. >>> >>> Greetings! >>> >>> On Wed, Dec 14, 2011 at 4:18 AM, Douglas Greve >>> <greve(a)nmr.mgh.harvard.edu >>> <mailto:greve@nmr.mgh.harvard.edu>> wrote: >>> >>> Try tksurfer Sub_ID lh inflated -annot seg.annot >>> doug >>> >>> >>> On 12/13/11 9:39 PM, vin . wrote: >>>> no, in tksurfer, just inflated lh appears (no >>>> overlay). so, I viewed lh.seg.mgh in freeview and >>>> converted it to .nii and viewed in fslview. >>>> >>>> On Wed, Dec 14, 2011 at 3:37 AM, Bruce Fischl >>>> <fischl(a)nmr.mgh.harvard.edu >>>> <mailto:fischl@nmr.mgh.harvard.edu>> wrote: >>>> >>>> oh, so you mean you see a line on the surface? >>>> >>>> On Wed, 14 Dec 2011, vin . wrote: >>>> >>>> Thanx Bruce for quick reply. >>>> >>>> you are right, it's surface based file after >>>> mri_vol2surf. yeah, tried with >>>> following command. >>>> >>>> >tksurfer Sub_ID lh inflated -annot >>>> lh.seg.annot -ov lh.seg.mgh -fthresh >>>> 0.01 -fmid 0.3 -fslope 1 >>>> >>>> >>>> On Wed, Dec 14, 2011 at 3:33 AM, Bruce Fischl >>>> <fischl(a)nmr.mgh.harvard.edu >>>> <mailto:fischl@nmr.mgh.harvard.edu>> >>>> wrote: >>>> Hi Vin >>>> >>>> it looks like your lh.seg.mgh is a >>>> surface-based .mgz not a >>>> volume one. Did you try loading it into >>>> tksurfer? >>>> >>>> cheers >>>> Bruce >>>> >>>> On Wed, 14 Dec 2011, vin . wrote: >>>> >>>> Thank you Doug, >>>> >>>> >tkregister2 --mov $d/T1.nii.gz --targ >>>> $d/mri/brain.mgz \ >>>> --regheader --reg $d/register.dat >>>> --noedit >>>> >>>> after creating register.dat, I >>>> followed the >>>> explained procedure, >>>> Which resulted in "lh.seg.mgh". >>>> can't view this >>>> file. ( appears a line ) >>>> >>>> >mri_info lh.seg.mgh >>>> Volume information for lh.seg.mgh >>>> type: MGH >>>> dimensions: 163842 x 1 x 1 x 17 >>>> voxel sizes: 1.0000, 1.0000, 1.0000 >>>> type: FLOAT (3) >>>> fov: 163842.000 >>>> >>>> >mri_info 3b.nii >>>> Volume information for 3b.nii >>>> type: nii >>>> dimensions: 182 x 218 x 182 >>>> voxel sizes: 1.0000, 1.0000, 1.0000 >>>> >>>> #binary maps looks okay >>>> >>>> may be I am doing mistake in >>>> registration or >>>> mri_vol2surf ? >>>> >mri_vol2surf --reg register.dat >>>> --mov Nb.nii >>>> --interp nearest --hemi lh --o >>>> lh.Nb.mgh >>>> >>>> Greetings! >>>> >>>> On Tue, Dec 13, 2011 at 5:56 PM, >>>> Douglas N Greve >>>> <greve(a)nmr.mgh.harvard.edu >>>> <mailto:greve@nmr.mgh.harvard.edu>> >>>> wrote: >>>> It's a little involved but >>>> possible. >>>> 1. Binarize Nth cluster to have >>>> a binary value >>>> of N >>>> mri_binarize --i N.nii >>>> --min 0.5 --binval N >>>> --o Nb.nii >>>> 2. Sample Nth cluster to the >>>> surface >>>> mri_vol2surf --reg >>>> register.dat --mov >>>> Nb.nii --interp >>>> nearest --hemi lh lh.Nb.mgh >>>> After doing that will all >>>> clusters, combine >>>> them together with >>>> mri_concat lh.1b.mgh >>>> lh.2b.mgh ... --vote >>>> --o lh.seg.mgh >>>> Now create a surface annotation >>>> mris_seg2annot --seg >>>> lh.seg.mgh --hemi lh --s >>>> subject --o >>>> lh.seg.annot --ctab yourctab >>>> yourctab is a color table like >>>> $FREESURFER_HOME/ >>>> FreeSurferColorLUT.txt. You >>>> >>>> list your regions >>>> and give them the colors you want. >>>> >>>> doug >>>> >>>> vin . wrote: >>>> Hi Doug, >>>> sorry for confusing names. >>>> >>>> - 1.nii is name of the >>>> cluster, which I >>>> want to >>>> overlay. it's a coritical >>>> region, >>>> resulted from >>>> fsl-probtrackx. >>>> I want to have few color >>>> codes in RGB >>>> R G B >>>> 1. 255 0 255 >>>> 2. 116 0 116 >>>> 3. 0 0 255 >>>> ... >>>> >>>> in this way, I would like >>>> to overlay 20 >>>> cortical >>>> regions in different >>>> colours on inflated >>>> brain. >>>> >>>> -fthresh 0.3 here >>>> (1/(10^0.3) == 50.12 % >>>> in freesurfer email >>>> archieve, I found >>>> this. hope >>>> it's correct. >>>> >>>> Thank you >>>> >>>> >>>> >>>> >>>> On Mon, Dec 12, 2011 at 11:11 PM, >>>> 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>>> >>>> wrote: >>>> >>>> Hi Vin, why do you say it's a 50% >>>> threshold? What >>>> is the >>>> 1.nii >>>> data? What colors do you want? >>>> doug >>>> >>>> vin . wrote: >>>> >>>> Dear FreeSurfer list, >>>> Greetings! >>>> >>>> a newbie to freesurfer. >>>> -- would like to overlay >>>> tracking group >>>> results (Sum from >>>> all >>>> subjects)-(from FSL ) in the >>>> inflated lh & >>>> rh. -- >>>> >>>> - it works with one region >>>> (hope it's >>>> correct), with >>>> following command, where, >>>> -fthresh ?? means >>>> it shows 50 % >>>> threshold based on intensity >>>> / only voxels >>>> which are >>>> overlaid >>>> by atleast half of the >>>> subjects ?? >>>> >>>> >tksurfer #Sub_ID lh inflated >>>> -annot >>>> aparc.annot -ov >>>> 1.nii >>>> -ovreg register.dat >>>> -fthresh 0.3 -fmid 0.3 >>>> -fslope 1 >>>> >>>> - How I can overlay multiple >>>> regions, in >>>> specific >>>> colours, >>>> with 50% thr. ? , >>>> Thank you :) >>>> Vin >>>> ----------------------------- - >>>> ------------------------------ >>>> ------------ >>>> >>>> _____________________________ _ >>>> _________________ >>>> 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 >>>> <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/ >>>> <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/ >>>> <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>> >>>> >>>> >>>> >>>> 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 >>>> <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> >>>> >>>> >>>> >>>> >>>> >>>> >>> >> >> _______________________________________________ >> 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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Post-Doctoral Position in Neuroimaging at UCSD
by Amanda Bischoff-Grethe 14 Dec '11

14 Dec '11

Post-Doctoral Position in Neuroimaging on the role of Reward and Inhibition on Appetite Regulation and Behavior A full-time Post-Doctoral position is available to work with Drs. Walter Kaye, Amanda Bischoff-Grethe, and Martin Paulus, Department of Psychiatry, University of California, San Diego. The post-doctoral fellow will work on several NIMH-funded research projects to investigate how altered reward or inhibition contributes to disturbed appetite regulation and other behaviors in anorexia and bulimia nervosa. Applicants should have experience with fMRI such as data acquisition, processing, and analysis. Moreover, experience working with clinical populations, neuropsychological testing, or programming is desirable. The postdoctoral fellow will be encouraged to develop his or her own research projects that fit within the overall scope of the project. The position will entail immersion in MR image analysis using one or more software tools, including AFNI, FSL, SPM, FreeSurfer, and R. Imaging sessions will take place at UCSD’s Center for Functional MRI, which is equipped with two research-dedicated GE 3T short-bore scanners. Appointment length is up to 5 years and is based upon the NIH salary scale. The position is available immediately, or the summer of 2012, and applications will be accepted until the position is filled. To apply, please send a brief statement of research interest and goals, any selected reprints, CV, and names and addresses of three references. For additional information or to apply, contact: Walter Kaye, MD Professor of Psychiatry Director, UCSD Eating Disorder Research and Treatment Program UCSD Department of Psychiatry 8950 Villa La Jolla Dr. Suite C207 La Jolla, CA 92037 http://eatingdisorders.ucsd.edu wkaye(a)ucsd.edu -- Amanda Bischoff-Grethe Assistant Adjunct Professor UCSD 9500 Gilman Drive MC 0738 La Jolla, CA 92093-0738 Tel: 858-246-0604 Fax: 858-246-0556

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fmcsm5-all.text ::created when?
by swoodman＠nmr.mgh.harvard.edu 14 Dec '11

14 Dec '11

Hello, Just a quick question.. when is the file (within the bold subdirectories) fmcsm5(4)-all.txt made? Is it created as a result of running func2roi? Thank you! Sandra

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Re: [Freesurfer] convert surface label on to functional image
by Douglas N Greve 14 Dec '11

14 Dec '11

That is the "fill threshold". It indicates how many label points must fall into a voxel in order for that voxel to be considered part of the label. By default it is just over 0, meaning that even one label point falling into the voxel will make that voxel labeled. I would leave it like, look at the mask, and then reduce it if you want the mask to be a little bit smaller. doug Zhangyuanchao wrote: > Hi,doug, > > In the help page of mri_label2vol, I see the following information as > an example of the usage of this command: > > 2. Convert a surface label into a binary mask in the functional space. > Fill in all the cortical gray matter. Require that a functional voxel > be filled at least 30% by the label: > mri_label2vol --label lh-avg_central_sulcus.label --temp f.nii > --reg register.dat --fillthresh .3 --proj frac 0 1 .1 --subject > bert --hemi lh --o cent-lh.nii > > I noticed the option of fillthresh,I do not quite understand what is > the meaning of the parameter of fillthresh, whose default value is 0; > In your last email, you omit this option to use the default value. > I wonder whether this is too loose a threshold given that the > resolution of functional images are low. Is it possible that the > obtained mask contains voxels which are not gray matter? > I am not sure, I want to use this mask as seed region for further > analysis. Could you show me how to choose the correct threshold of the > fillthresh option? > > Thanks a lot for your kindness and patiency! > > Yuanchao > > --- *11年12月14日，周三, Douglas N Greve > /<greve(a)nmr.mgh.harvard.edu>/* 写道： > > > 发件人: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > 主题: Re: [Freesurfer] convert surface label on to functional image > 收件人: "Zhangyuanchao" <woshizhangyc(a)yahoo.cn>, "freesurfer" > <freesurfer(a)nmr.mgh.harvard.edu> > 日期: 2011年12月14日,周三,上午1:01 > > The easiest thing is to use mri_label2vol, something like > mri_label2vol --label yourlabel.label --temp functemplate.nii --reg > register.dat --proj frac 0 1 .1 --hemi lh --subject subject --o > yourlabel.nii > > doug > > Zhangyuanchao wrote: > > Thanks for your response! > > > > In fact, the label that I want to convert to functional space was > > obtained by between-group comparisons, so it does not belong to any > > existing parcellation template. > > > > What should I do in this case? > > > > Thanks! > > > > Best, > > > > --- *11年12月13日，周二, Douglas N Greve > > /<greve(a)nmr.mgh.harvard.edu > </mc/compose?to=greve(a)nmr.mgh.harvard.edu>>/* 写道： > > > > > > 发件人: Douglas N Greve <greve(a)nmr.mgh.harvard.edu > </mc/compose?to=greve(a)nmr.mgh.harvard.edu>> > > 主题: Re: [Freesurfer] convert surface label on to > functional image > > 收件人: "Zhangyuanchao" <woshizhangyc(a)yahoo.cn > </mc/compose?to=woshizhangyc(a)yahoo.cn>> > > 抄送: freesurfer(a)nmr.mgh.harvard.edu > </mc/compose?to=freesurfer(a)nmr.mgh.harvard.edu> > > 日期: 2011年12月13日,周二,上午5:48 > > > > Hi Yuanchao, I would recommend that you use the aparc+aseg.mgz > > file for this. This file has cortical labels already in the > > volume, you just need to map them to your functional space, > > something like > > > > mri_label2vol --aparc+aseg --temp functemplate.nii --reg > > register.dat --o aparc+aseg.fmri.nii > > > > doug > > > > Zhangyuanchao wrote: > > > hi, expert, > > > > > > By mapping a surface label to a functional template, I want to > > extract the corresponding cortical gray matter region in the > > functional space. I know I should use the mri_label2vol command. > > > In the help page of mri_label2vol, I see some examples of this > > command. > > > > > > 2. Convert a surface label into a binary mask in the > functional > > space. > > > Fill in all the cortical gray matter. Require that a > functional > > voxel > > > be filled at least 30% by the label: > > > > > > mri_label2vol --label lh-avg_central_sulcus.label --temp > > f.nii --reg register.dat --fillthresh .3 --proj frac 0 1 > > .1 --subject bert --hemi lh > > > --o cent-lh.nii > > > > > > 3. Convert a surface label into a binary mask in the > functional > > space. > > > Sample a 1mm ribbon 2mm below the gray/white surface. Do not > > require a fill threshold: > > > > > > mri_label2vol --label lh-avg_central_sulcus.label --temp > > f.nii --reg register.dat --proj abs -3 -2 .1 --subject > bert > > --hemi lh > > > --o cent-lh.nii > > > > > > I want to extract the cortical gray matter on the functional > > images corresponding to the surface label. I do not know > which of > > the above commands could obtain the result I want and which > > parameters I should use to obtain what I want. > > > > > > For example 3, I do not quite catch what "Sample a 1mm ribbon > > 2mm below the gray/white surface. " this sentence means. > > > Thanks for your help! > > > > > > > > > Best > > > > > > Yuanchao > > > > > > > > > ------------------------------------------------------------------------ > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu > </mc/compose?to=Freesurfer(a)nmr.mgh.harvard.edu> > > </mc/compose?to=Freesurfer(a)nmr.mgh.harvard.edu > </mc/compose?to=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 > </mc/compose?to=greve(a)nmr.mgh.harvard.edu> > </mc/compose?to=greve(a)nmr.mgh.harvard.edu > </mc/compose?to=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 > > > > > > > > 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 </mc/compose?to=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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average subject
by Fariba Sharifian 14 Dec '11

14 Dec '11

Hi, I have used make_average_subject and made a new average subject form my N subjects, now I want to load one overlay form a single subject on this new average subject, how should I do that? Regards, Fariba __________________________________________________ Fariba Sharifian, PhD Student. Vision Systems Physiology group, Brain research unit Low Temperature Laboratory and AMI centre Aalto University School of Science and Technology PO BOX 13000, FI-00076 Aalto Espoo, Finland tel: +358-9-470 26159 fax: +358-9-470 22969 e-mail:fariba@neuro.hut.fi http://ltl.tkk.fi/wiki/BRU/Vision_Systems_Physiology __________________________________________________ Fariba Sharifian, PhD Student. Vision Systems Physiology group, Brain research unit Low Temperature Laboratory and AMI centre Aalto University School of Science and Technology PO BOX 13000, FI-00076 Aalto Espoo, Finland tel: +358-9-470 26159 fax: +358-9-470 22969 e-mail:fariba@neuro.hut.fi http://ltl.tkk.fi/wiki/BRU/Vision_Systems_Physiology

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spgr orientation and re-slicing
by Cat Chong 14 Dec '11

14 Dec '11

Dear Experts, I am sorry for the basic question but we have a dataset of subjects we like to analyze for which we have different slice thicknesses and orientations in dicom format. All T1's collected were SPGR volumes with the same scanner parameters. My question was: Do you advice to re-orient and re-slice the dataset to make it uniform or is that step not necessary cheers and thank you catherine

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dt_recon error
by Yuko Yotsumoto 14 Dec '11

14 Dec '11

Hello, I'm having a problem with dt_recon on data scanned by Siemens TrioTim. I'm using v4.5.0, with Mac OS 10.6.8. dt_recon ran for a while, and stopped with an error "ERROR: cannot extract sWiPMemBlock.alFree[8] from /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-infodump.dat" I found the same errors reported to this mailing list, but found no solution. https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-August/019755.h… http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07935.html In YDTI/YD11A/ folder, I have the following files dt_recon.log dwi-ec.ecclog dwi-ec.nii dwi-infodump.dat dwi.nii mri_glmfit.log In dwi-infodump.dat, I see bunch of lines, but I don't see "sWiPMemBlock.alFree". Please help! Thanks, Yuko Yotsumoto #@#------------------------------- Fitting Tensors Wed Dec 7 10:15:52 JST 2011 cd /Users/yuko/Documents/FreeSurfer/subjects mri_glmfit --y /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec.nii --glmdir /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A --dti /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-infodump.dat $Id: mri_glmfit.c,v 1.138.2.15 2009/07/27 17:43:10 greve Exp $ cwd /Users/yuko/Documents/FreeSurfer/subjects cmdline mri_glmfit --y /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec.nii --glmdir /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A --dti /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-infodump.dat sysname Darwin hostname Yukos-iMac.local machine i386 user yuko FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec.nii logyflag 1 X /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-infodump.dat usedti 1 glmdir /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A IllCondOK 0 DoFFx 0 Creating output directory /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A Loading y from /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec.nii Using DTI bValue = 700 ERROR: cannot extract sWiPMemBlock.alFree[8] from /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-infodump.dat

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Re: [Freesurfer] multiple overlay - tksurfer
by Douglas Greve 14 Dec '11

14 Dec '11

The fsaverage surface does not intersect very well with the MNI brain (the problem is that the average surface does not have as deep folds as an individual). You can see what is going on if you convert your label to fsaverage space with tkmedit fsaverage orig.mgz -surfs -fmin 0.5 -overlay 1.nii -overlay-reg register.dat This will show you the surfaces and the label. If the label does not intersect the surfaces, at all, then there's not much you can do. If there is some intersection, then you can run mri_vol2surf with --projfrac-max -.1 1.1 .1 doug On 12/13/11 10:53 PM, vin . wrote: > #Registration > >tkregister2 --mov $d/T1.nii.gz --targ > $d/mri/brain.mgz \ > --regheader --reg $d/vin_register.dat --noedit > > I have cortical-clusters in 1mm MNI space so, I took 1mm MNI brain and > registered this on the "fsaverage" default subject's /mri/brain.mgz" > > Find attached register.dat > > #checking registration > > > tkregister2 --targ $d/mri/brain.mgz \ > --mov T1.nii.gz --reg vin_register.dat > > find attached register.tiff > > Regards, > vin > > > On Wed, Dec 14, 2011 at 4:40 AM, Douglas Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > Is your register.dat correct? > > > On 12/13/11 10:33 PM, vin . wrote: >> Thanx Doug, >> >> atleast I see, now something. (see attached "seg.mgh -annot >> seg.annot.tiff) >> > tksurfer Sub_ID lh inflated -annot seg.annot -ov lh.seg.mgh >> -fthresh 0.01 -fmid 0.3 -fslope 1 >> >> just to check, I also summed, all binary files. (attached >> sum_binarymap) >> >tksurfer Sub_ID lh inflated -ov sum_binmap.nii -overlay-reg >> register.dat -fthresh 0.01 -fmid 0.3 -fslope 1 >> >> also find colortable. >> >> Greetings! >> >> On Wed, Dec 14, 2011 at 4:18 AM, Douglas Greve >> <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: >> >> Try tksurfer Sub_ID lh inflated -annot seg.annot >> doug >> >> >> On 12/13/11 9:39 PM, vin . wrote: >>> no, in tksurfer, just inflated lh appears (no overlay). so, >>> I viewed lh.seg.mgh in freeview and converted it to .nii >>> and viewed in fslview. >>> >>> On Wed, Dec 14, 2011 at 3:37 AM, Bruce Fischl >>> <fischl(a)nmr.mgh.harvard.edu >>> <mailto:fischl@nmr.mgh.harvard.edu>> wrote: >>> >>> oh, so you mean you see a line on the surface? >>> >>> On Wed, 14 Dec 2011, vin . wrote: >>> >>> Thanx Bruce for quick reply. >>> >>> you are right, it's surface based file after >>> mri_vol2surf. yeah, tried with >>> following command. >>> >>> >tksurfer Sub_ID lh inflated -annot lh.seg.annot -ov >>> lh.seg.mgh -fthresh >>> 0.01 -fmid 0.3 -fslope 1 >>> >>> >>> On Wed, Dec 14, 2011 at 3:33 AM, Bruce Fischl >>> <fischl(a)nmr.mgh.harvard.edu >>> <mailto:fischl@nmr.mgh.harvard.edu>> >>> wrote: >>> Hi Vin >>> >>> it looks like your lh.seg.mgh is a >>> surface-based .mgz not a >>> volume one. Did you try loading it into tksurfer? >>> >>> cheers >>> Bruce >>> >>> On Wed, 14 Dec 2011, vin . wrote: >>> >>> Thank you Doug, >>> >>> >tkregister2 --mov $d/T1.nii.gz --targ >>> $d/mri/brain.mgz \ >>> --regheader --reg $d/register.dat --noedit >>> >>> after creating register.dat, I followed the >>> explained procedure, >>> Which resulted in "lh.seg.mgh". can't >>> view this >>> file. ( appears a line ) >>> >>> >mri_info lh.seg.mgh >>> Volume information for lh.seg.mgh >>> type: MGH >>> dimensions: 163842 x 1 x 1 x 17 >>> voxel sizes: 1.0000, 1.0000, 1.0000 >>> type: FLOAT (3) >>> fov: 163842.000 >>> >>> >mri_info 3b.nii >>> Volume information for 3b.nii >>> type: nii >>> dimensions: 182 x 218 x 182 >>> voxel sizes: 1.0000, 1.0000, 1.0000 >>> >>> #binary maps looks okay >>> >>> may be I am doing mistake in registration or >>> mri_vol2surf ? >>> >mri_vol2surf --reg register.dat --mov Nb.nii >>> --interp nearest --hemi lh --o >>> lh.Nb.mgh >>> >>> Greetings! >>> >>> On Tue, Dec 13, 2011 at 5:56 PM, Douglas >>> N Greve >>> <greve(a)nmr.mgh.harvard.edu >>> <mailto:greve@nmr.mgh.harvard.edu>> >>> wrote: >>> It's a little involved but possible. >>> 1. Binarize Nth cluster to have a >>> binary value >>> of N >>> mri_binarize --i N.nii --min 0.5 >>> --binval N >>> --o Nb.nii >>> 2. Sample Nth cluster to the surface >>> mri_vol2surf --reg register.dat >>> --mov >>> Nb.nii --interp >>> nearest --hemi lh lh.Nb.mgh >>> After doing that will all clusters, >>> combine >>> them together with >>> mri_concat lh.1b.mgh lh.2b.mgh >>> ... --vote >>> --o lh.seg.mgh >>> Now create a surface annotation >>> mris_seg2annot --seg lh.seg.mgh >>> --hemi lh --s >>> subject --o >>> lh.seg.annot --ctab yourctab >>> yourctab is a color table like >>> $FREESURFER_HOME/ >>> FreeSurferColorLUT.txt. You >>> >>> list your regions >>> and give them the colors you want. >>> >>> doug >>> >>> vin . wrote: >>> Hi Doug, >>> sorry for confusing names. >>> >>> - 1.nii is name of the >>> cluster, which I >>> want to >>> overlay. it's a coritical region, >>> resulted from >>> fsl-probtrackx. >>> I want to have few color codes >>> in RGB >>> R G B >>> 1. 255 0 255 >>> 2. 116 0 116 >>> 3. 0 0 255 >>> ... >>> >>> in this way, I would like to >>> overlay 20 >>> cortical >>> regions in different colours >>> on inflated >>> brain. >>> >>> -fthresh 0.3 here >>> (1/(10^0.3) == 50.12 % >>> in freesurfer email archieve, >>> I found >>> this. hope >>> it's correct. >>> >>> Thank you >>> >>> >>> >>> >>> On Mon, Dec 12, 2011 at 11:11 PM, 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>>> >>> wrote: >>> >>> Hi Vin, why do you say it's a 50% >>> threshold? What >>> is the >>> 1.nii >>> data? What colors do you want? >>> doug >>> >>> vin . wrote: >>> >>> Dear FreeSurfer list, >>> Greetings! >>> >>> a newbie to freesurfer. >>> -- would like to overlay tracking >>> group >>> results (Sum from >>> all >>> subjects)-(from FSL ) in the >>> inflated lh & >>> rh. -- >>> >>> - it works with one region (hope it's >>> correct), with >>> following command, where, -fthresh >>> ?? means >>> it shows 50 % >>> threshold based on intensity / >>> only voxels >>> which are >>> overlaid >>> by atleast half of the subjects ?? >>> >>> >tksurfer #Sub_ID lh inflated -annot >>> aparc.annot -ov >>> 1.nii >>> -ovreg register.dat -fthresh >>> 0.3 -fmid 0.3 >>> -fslope 1 >>> >>> - How I can overlay multiple >>> regions, in >>> specific >>> colours, >>> with 50% thr. ? , >>> Thank you :) >>> Vin >>> ----------------------------- - >>> ------------------------------ >>> ------------ >>> >>> _____________________________ _ >>> _________________ >>> 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 >>> <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/ >>> <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/ >>> <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>> >>> >>> >>> >>> 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 >>> <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> >>> >>> >>> >>> >>> >>> >> > > _______________________________________________ > 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. > >

1 0

Re: [Freesurfer] multiple overlay - tksurfer
by Douglas Greve 13 Dec '11

13 Dec '11

Is your register.dat correct? On 12/13/11 10:33 PM, vin . wrote: > Thanx Doug, > > atleast I see, now something. (see attached "seg.mgh -annot > seg.annot.tiff) > > tksurfer Sub_ID lh inflated -annot seg.annot -ov lh.seg.mgh -fthresh > 0.01 -fmid 0.3 -fslope 1 > > just to check, I also summed, all binary files. (attached sum_binarymap) > >tksurfer Sub_ID lh inflated -ov sum_binmap.nii -overlay-reg > register.dat -fthresh 0.01 -fmid 0.3 -fslope 1 > > also find colortable. > > Greetings! > > On Wed, Dec 14, 2011 at 4:18 AM, Douglas Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > Try tksurfer Sub_ID lh inflated -annot seg.annot > doug > > > On 12/13/11 9:39 PM, vin . wrote: >> no, in tksurfer, just inflated lh appears (no overlay). so, I >> viewed lh.seg.mgh in freeview and converted it to .nii and >> viewed in fslview. >> >> On Wed, Dec 14, 2011 at 3:37 AM, Bruce Fischl >> <fischl(a)nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> >> wrote: >> >> oh, so you mean you see a line on the surface? >> >> On Wed, 14 Dec 2011, vin . wrote: >> >> Thanx Bruce for quick reply. >> >> you are right, it's surface based file after >> mri_vol2surf. yeah, tried with >> following command. >> >> >tksurfer Sub_ID lh inflated -annot lh.seg.annot -ov >> lh.seg.mgh -fthresh >> 0.01 -fmid 0.3 -fslope 1 >> >> >> On Wed, Dec 14, 2011 at 3:33 AM, Bruce Fischl >> <fischl(a)nmr.mgh.harvard.edu >> <mailto:fischl@nmr.mgh.harvard.edu>> >> wrote: >> Hi Vin >> >> it looks like your lh.seg.mgh is a surface-based >> .mgz not a >> volume one. Did you try loading it into tksurfer? >> >> cheers >> Bruce >> >> On Wed, 14 Dec 2011, vin . wrote: >> >> Thank you Doug, >> >> >tkregister2 --mov $d/T1.nii.gz --targ >> $d/mri/brain.mgz \ >> --regheader --reg $d/register.dat --noedit >> >> after creating register.dat, I followed the >> explained procedure, >> Which resulted in "lh.seg.mgh". can't view this >> file. ( appears a line ) >> >> >mri_info lh.seg.mgh >> Volume information for lh.seg.mgh >> type: MGH >> dimensions: 163842 x 1 x 1 x 17 >> voxel sizes: 1.0000, 1.0000, 1.0000 >> type: FLOAT (3) >> fov: 163842.000 >> >> >mri_info 3b.nii >> Volume information for 3b.nii >> type: nii >> dimensions: 182 x 218 x 182 >> voxel sizes: 1.0000, 1.0000, 1.0000 >> >> #binary maps looks okay >> >> may be I am doing mistake in registration or >> mri_vol2surf ? >> >mri_vol2surf --reg register.dat --mov Nb.nii >> --interp nearest --hemi lh --o >> lh.Nb.mgh >> >> Greetings! >> >> On Tue, Dec 13, 2011 at 5:56 PM, Douglas N Greve >> <greve(a)nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu>> >> wrote: >> It's a little involved but possible. >> 1. Binarize Nth cluster to have a binary >> value >> of N >> mri_binarize --i N.nii --min 0.5 >> --binval N >> --o Nb.nii >> 2. Sample Nth cluster to the surface >> mri_vol2surf --reg register.dat --mov >> Nb.nii --interp >> nearest --hemi lh lh.Nb.mgh >> After doing that will all clusters, combine >> them together with >> mri_concat lh.1b.mgh lh.2b.mgh ... --vote >> --o lh.seg.mgh >> Now create a surface annotation >> mris_seg2annot --seg lh.seg.mgh --hemi >> lh --s >> subject --o >> lh.seg.annot --ctab yourctab >> yourctab is a color table like >> $FREESURFER_HOME/ FreeSurferColorLUT.txt. >> You >> >> list your regions >> and give them the colors you want. >> >> doug >> >> vin . wrote: >> Hi Doug, >> sorry for confusing names. >> >> - 1.nii is name of the cluster, >> which I >> want to >> overlay. it's a coritical region, >> resulted from >> fsl-probtrackx. >> I want to have few color codes in RGB >> R G B >> 1. 255 0 255 >> 2. 116 0 116 >> 3. 0 0 255 >> ... >> >> in this way, I would like to overlay 20 >> cortical >> regions in different colours on >> inflated >> brain. >> >> -fthresh 0.3 here >> (1/(10^0.3) == 50.12 % >> in freesurfer email archieve, I found >> this. hope >> it's correct. >> >> Thank you >> >> >> >> >> On Mon, Dec 12, 2011 at 11:11 PM, 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>>> >> wrote: >> >> Hi Vin, why do you say it's a 50% >> threshold? What >> is the >> 1.nii >> data? What colors do you want? >> doug >> >> vin . wrote: >> >> Dear FreeSurfer list, >> Greetings! >> >> a newbie to freesurfer. >> -- would like to overlay tracking group >> results (Sum from >> all >> subjects)-(from FSL ) in the inflated lh & >> rh. -- >> >> - it works with one region (hope it's >> correct), with >> following command, where, -fthresh ?? means >> it shows 50 % >> threshold based on intensity / only voxels >> which are >> overlaid >> by atleast half of the subjects ?? >> >> >tksurfer #Sub_ID lh inflated -annot >> aparc.annot -ov >> 1.nii >> -ovreg register.dat -fthresh 0.3 >> -fmid 0.3 >> -fslope 1 >> >> - How I can overlay multiple regions, in >> specific >> colours, >> with 50% thr. ? , >> Thank you :) >> Vin >> ----------------------------- - >> ------------------------------ >> ------------ >> >> _____________________________ _ >> _________________ >> 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 >> <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/ >> <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/ >> <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>> >> >> >> >> 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 >> <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> >> >> >> >> >> >> >

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Freesurfer December 2011