Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

jittered ITI and null trials
by Lukito, Steve 12 Aug '13

12 Aug '13

Hi there, Please ignore my earlier question. The Cygwin is still a mystery to me but I have managed to run the optseq2 on a UNIX computer. It seems there is no way to input jittered ITI and null trials at the same time in optseq2, is this right? This is because null trials by definition is equal to jitter (this is how I understand Douglas Greve's slides). Unfortunately, I would like to replicate an experiment with three experimental conditions with four types of trials (=the exp conditions plus null trials). Each trial is jittered so that its length is between 2850 and 3350 ms long, which include the 1000 ms stimulus presentation. My thought is to use psdwin=0 - 1850 ms (2850 ms minus 1000 ms stim presentation) for now and then later on replace this constant time window with the jittered ones (randomized). I assume that if I can build an optimum sequence for the shorter boundary of the ITI, they will still be as optimum when I replace the post-stimulus time window with the jittered one provided that the jittered time interval is of longer span. I am not sure if this is even remotely true so I would really appreciate anyone's comment on this. Best, Steve

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editing topological defect
by pietro de rossi 12 Aug '13

12 Aug '13

Hi freesurfers, I have a problem editing a topological defect given that it is represented by cortex non included within the pial boundary without white matter in it. The problem is I can't use white matter to place control points and/or edit voxel in the aux wm.mgz volume... I'm attaching an image... the area I'm talking about is indicated by green arrows. Thanks in advance, Pietro -- Pietro De Rossi, MD ------------------------------------- Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma NESMOS Department (Neurosciences, Mental Health and Sensory Functions), School of Medicine and Psychology, Sapienza University, Sant’Andrea Hospital, Via di Grottarossa 1035-1039, 00189 Rome, Italy Neurobehavioral Clinical Research Section, Social and Behavioral Research Branch, National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA

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Validation of results
by Sinead Kelly 12 Aug '13

12 Aug '13

Dear freesurfer users, I would really appreciate if anybody could confirm that I have preformed my analysis correctly as I have very little experience with freesurfer and I want to make sure that my result is a true finding. Firstly, I am looking at the effect of a schizophrenia risk variant on cortical surface area in a large sample of healthy controls. a. I performed preprocessing on all of my subjects using *recon-all.* b. I then qcached my data (resampling it to the average subject -* fsaverage *) c. An FSGD file was then created for statistical analysis to look at differences between TT carriers and TG carriers with age and gender as covariates of no interest. Here is an example of the file I created: GroupDescriptorFile 1 Title MIR137 Class TTMale Class TTFemale Class TGMale Class TGFemale Variables Age Input CON3140 TGFemale 37 Input CON3891 TTFemale 33 Input CON4664 TTFemale 40 Input CON5591 TTMale 41 Input CON7009 TGMale 21 Input CON7024 TTMale 59 Input CON7038 TTMale 56 Input CON7050 TTMale 30 Input CON7054 TTMale 43 Input CON7055 TTMale 43 Input CON7072 TTFemale 41 d. I applied the following contrast: -0.5 -0.5 0.5 0.5 0 0 0 0 e. I followed the online tutorial by firstly running the *mris_preproc*script with *area.fwhm10.fsaverage* as my input file. Is this correct? (I ran this separately for the left and right hemisphere). f. I then ran the *mri_glmfi*t script followed by the *mri_glmfit-sim*script: *mri_glmfit-sim --glmdir rh.MIR137_area.glmdir --sim mc-z 5000 1.3 mc-z.abs --sim-sign abs --cwpvalthresh .999 --overwrite* (I ran this separately for each hemisphere) Does this look correct? When this ran I then checked the *mc-z.abs.sig.cluster.summary file:* ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs Annot 1 -3.298 36614 541.01 -26.0 -53.1 62.2 0.77340 0.76580 0.78100 1177 superiorparietal 2 2.918 9004 1642.43 -8.5 9.7 65.2 *0.01020* 0.00840 0.01200 2790 superiorfrontal 3 2.626 126211 363.55 -30.3 -65.2 40.5 0.98580 0.98360 0.98800 817 inferiorparietal 4 2.441 6490 313.02 -30.5 -35.1 58.4 0.99660 0.99560 0.99760 693 postcentral 5 2.375 107140 1095.56 -10.9 -57.2 44.7 0.09720 0.09180 0.10260 2308 precuneus 6 2.347 132687 414.79 -38.6 2.1 24.8 0.95300 0.94920 0.95680 974 precentral 7 2.284 97632 1510.86 -41.4 -50.0 -14.4 *0.01820* 0.01580 0.02060 2446 fusiform 8 2.122 111909 365.94 -49.2 -29.5 -3.0 0.98480 0.98260 0.98700 837 superiortemporal 9 2.070 74111 444.95 -54.7 -42.0 6.3 0.92120 0.91620 0.92600 998 bankssts 10 1.809 85712 281.07 -57.0 -30.8 21.7 0.99860 0.99800 0.99920 598 supramarginal 11 1.796 121724 312.87 -10.0 64.3 6.5 0.99660 0.99560 0.99760 485 superiorfrontal I have two significant results here - does this look okay? Does this result indicate that surface area of the fusiform and superior frontal significantly differ between TT and TG carriers (corrected for multiple comparisons?). How can I check or report the statistics? Is it possible to extract the values and report descriptive as well as inferential statistics for the result? I would really appreciate if anyone can validate this for me as I have very little experience with freesurfer. Thank you for your help! Sinead Sinead Kelly Neuropsychiatric Genetics Group Trinity Centre St. James's Hospital Dublin 8

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Re: [Freesurfer] mean thickness over hemisphere in stats file
by Bruce Fischl 12 Aug '13

12 Aug '13

Hi Ines sorry, this was my mistake. The command is "mris_anatomical_stats" NOT "mris_anatomical_thickness". If your SUBJECTS_DIR is set properly, you can run: mris_anatomical_stats -l $SUBJECTS_DIR/$subject/label/$hemi.cortex \ $subject $hemi where $hemi is lh or rh and $subject is the subject id you want to quantify cheers Bruce On Mon, 12 Aug 2013, Mürner-Lavanchy, Ines wrote: > ________________________________________ > From: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] > Sent: Friday, 9 August 2013 3:36 PM > To: Mürner-Lavanchy, Ines > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] mean thickness over hemisphere in stats file > > Hi Ines > > I think mris_anatomical_thickness is your best bet. You probably want to > specify the ?h.cortex.label file with the -l flag so that it ignores > non-cortical regions > > cheers > Bruce > > > On Fri, 9 Aug 2013, Mürner-Lavanchy, Ines wrote: > >> Dear experts, >> >> please excuse my question, I'm a beginner. I really searched for an answer >> in the archive, but I couldn't find out what I was doing wrong. >> >> I would like to write the mean cortical thickness of a hemisphere in the >> stats file. I read one can do that by using -m thickness. >> Where in the command line do I have to put it? I tried various versions, but >> it doesn't work. >> >> This would be the command: >> >> aparcstats2table --hemi rh --parc aparc --meas thickness --tablefile >> "directory"//"filename" --m thickness --subjects 1 2 3 4 >> SUBJECTS_DIR : "directory" >> >> Where do I include the -m thickness option? Or do I have to add something >> else? >> >> Thank you very much for your help, >> Ines >> >> > > > 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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Optseq2 with Cygwin
by Lukito, Steve 12 Aug '13

12 Aug '13

Dear optseq2 developers, I would like to use optseq2 to develop optimal sequence for my MRI experiment. I have a windows machine (Windows 7, SP1, 64-bit OS) so I installed Cygwin-64 to run the optseq2. What I've done so far: - Downloaded optseq2.exe (Cygwin version) and put this into the Cygwin-64 folder - I run Cygwin and change my directory to Cygwin-64 where the optseq2 is - I followed instructions from previous email trails so I typed in chmod a+x optseq2 (to make optseq2 executable within the shell?) - Then I typed in ./optseq2 (since typing in optseq2 on its own results in -bash: optseq2: command not found) On both occasions (chmod... and ./optseq2), the command prompt returns without output. As I understand it, at least, for the second command I should get the help text for optseq? Have I done something wrong? Would really appreciate you help! Steve PS I am not familiar with UNIX so please be patient if my question is trivial :). Steve Lukito, MSc. PhD Candidate | Institute of Psychiatry | King's College London Department of Child and Adolescent Psychiatry - PO85 16 De Crespigny Park London SE5 8AF Phone: 0207 848 0469

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Re: [Freesurfer] trac-all inquiry
by Anastasia Yendiki 12 Aug '13

12 Aug '13

When you apply a rotation to the DWIs (as eddy_correct does), you need to apply the same rotation to the corresponding gradient vectors. See for example: Leemans, A., Jones, D. K., Jun 2009. The B-matrix must be rotated when correcting for subject motion in DTI data. Magn Reson Med 61 (6), 1336–49. If you don't want to pass the dicoms to trac-all directly, you can use mri_convert to convert from dicom to nifti. On Fri, 9 Aug 2013, Soto, David wrote: > hi - am afraid not because I am feeding to trac-all > already eddycorrected images then in the config file > I have > > # Perform registration-based eddy-current compensation? > # Default: 1 (yes) > set doeddy = 0 > # Rotate diffusion gradient vectors to match eddy-current compensation? > # Only used if doeddy = 1 > # Default: 1 (yes) > > is this critical?? > > unfortunately, this is the only way I manage to get it to work > as said my diffusion outputs from mriconverter > are not read by FS, only through mediation > of some FSL operation on the files, then FS > likes those. > > I could start from scratch using dicoms but would prefer > not to as the data is already well organised > > cheers > ds > http://www1.imperial.ac.uk/medicine/people/d.soto/ > > ________________________________________ > From: Anastasia Yendiki [ayendiki(a)nmr.mgh.harvard.edu] > Sent: 09 August 2013 22:44 > To: Soto, David > Subject: Re: [Freesurfer] trac-all inquiry > > Are you rotating the gradient vectors accordingly? This is done in > trac-all after running eddy_correct. > > On Fri, 9 Aug 2013, Soto, David wrote: > >> Hi Anastasia, stuff is running smoothly at last one quick question, is there >> any 'disadvantage' in >> using FSL to do the eddy correct and then feed >> those images to trace-all ? >> cheers >> ds >> http://www1.imperial.ac.uk/medicine/people/d.soto/ >> >> On 9 Aug 2013, at 15:33, David Soto <dsoto(a)imperial.ac.uk> >> wrote: >> >> hi, for some reason FS does not like the >> nii file from Mriconverter, ( I saw >> a post about this >> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg19526.html >> ) but does like >> the nii.gz outputs from FSL... >> >> I'll try to debug the bepostx error >> >> thanks! >> >> ds >> >> http://www1.imperial.ac.uk/medicine/people/d.soto/ >> On 09/08/13 14:26, Anastasia Yendiki wrote: >> >> There is no reason to conevrt to .mnc. You should use your >> original .nii, if that shows up correctly in freeview. >> >> As for the bedpostx error, this is an Ubuntu issue that >> has come to my attention very recently. In Ubuntu /bin/sh >> is not a bash shell any more. To get around this, you'll >> have to edit the first line of the scripts >> $FREESURFER_HOME/bin/bedpostx_mgh and >> $FREESURFER_HOME/bin/fsl_sub_mgh. You'll have to replace >> "/bin/sh" with "/bin/bash" on the first line of those two >> scripts. >> >> On Fri, 9 Aug 2013, David Soto wrote: >> >> hi- I tried to convert from nii to mnc becos >> that is what i did when >> I did recon-all >> >> but I also tried with nii at the beggining and >> got the same issues. >> In fact in my last post (pasted below >> again)the input was a nii file >> could you please check the stuff below? >> thanks! ds >> >> >> Hi, further to my prior email >> I made some progress. I noted that nii2mnc >> does not seem to work on the diffusion >> output.nii that I got from Mriconverter as the >> output.mnc brain has parts chopped in >> Freeview. >> >> (I think there may be something funny about >> this, as the recon-all does like the T1 output >> form Mriconverter) >> >> HENCE I tried use the output of eddycorrect >> from FSL (which I already run for other thing) >> Then I created a new folder where i placed the >> output of FSL eddycorrect and in the >> configuration file I did >> (i) set dcmlist = >> (fsleddycorrectoutput.nii.gz) >> (ii) turned 'set doeddy = 0' >> >> then run it >> trac-all -c traculatest.txt -prep -log >> trac_from_fsleddy >> >> >> it seemed to complete without errors (log >> attached)n and I checked the preprocessing >> outputs in Freeview (FA, masks and >> aparc+asegs) and all seemed >> fine. >> >> However when I attempt the next stage in >> trac-all >> i.e. trac-all -c traculatest.txt -bedp -log >> trac_from_fsleddy_bedp >> it fails saying the following >> /usr/local/freesurfer/bin/bedpostx_mgh: 131: >> /usr/local/freesurfer/bin/bedpostx_mgh: Syntax >> error: "(" unexpected >> >> >> the log is also attached. >> >> any advise appreciated! >> >> cheers >> ds >> http://www1.imperial.ac.uk/medicine/people/d.soto/ >> http://www1.imperial.ac.uk/medicine/people/d.soto/ >> On 09/08/13 14:02, Anastasia Yendiki wrote: >> >> Why are you converting from .nii >> to .mnc? Why are you not using the >> .nii directly? >> >> On Fri, 9 Aug 2013, David Soto >> wrote: >> >> hi - thanks for the >> feedback >> >> weirdly, the nii2mnc >> transform of the >> diffusion >> data falters, I get a >> part of the brain >> chopped >> have no idea why this >> is the case, as it >> worked fine >> before for the T1 for >> recon-all...I am using >> Ubuntu 12.04 >> >> anyway am trying to >> sort this out now, if >> you have any >> advise that would much >> appreciated!! >> cheers >> ds >> >> >> http://www1.imperial.ac.uk/medicine/people/d.soto/ >> On 08/08/13 17:03, >> Anastasia Yendiki >> wrote: >> >> Hi David - >> The fact >> that it's >> taking so >> many tries >> to >> initialize >> the left >> ILF tells >> me that >> something >> has gone >> wrong with >> the data, >> either >> with the >> T1 to DWI >> registration, >> or with >> the mask, >> or >> something >> like that. >> Have you >> looked at >> any of the >> output >> files of >> the >> pre-processing? >> The FA >> map, the >> aparc+aseg, >> etc? >> >> a.y >> >> On Wed, 7 >> Aug 2013, >> Soto, >> David >> wrote: >> >> Hi >> Anastasia, >> I >> checked >> the >> becs >> and >> bvals >> files, >> there >> was >> a >> bug >> in >> the >> transposition >> of >> the >> columns >> into >> 3 >> rows >> in >> the >> bvecs. >> But >> i >> still >> have >> problems.. >> I >> rerun >> trac-all >> -prep >> and >> seemed >> fine >> but >> ended >> with >> a >> Segmentation >> fault >> (core >> dumped) >> which >> however >> is >> not >> present >> in >> the >> last >> line >> of >> the >> trac-all.log >> (Attached). >> Writing >> output >> files >> to/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/lh.ilf_AS_avg33_mn >> i_bbr_* >> Writing >> spline >> volume >> to/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/lh.ilf_AS_avg33_mn >> i_bbr_cpts_5.nii.gz >> Segmentation >> fault >> (core >> dumped) >> Just >> in >> case >> I >> tried >> trac-all >> -bedp >> complains >> like >> these >> below, >> any >> advise >> appreciated, >> cheers >> - >> ds >> /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/diffree/tracula02ST.txt >> -bedp >> INFO: >> SUBJECTS_DIR >> is >> /home/dsoto/Documents/fmri/rsdtianawmgui >> INFO: >> Diffusion >> root >> is >> /home/dsoto/Documents/fmri/rsdtianawmgui >> Actual >> FREESURFER_HOME >> /usr/local/freesurfer >> WARN: >> Running >> FSL's >> bedbost >> locally >> - >> this >> might >> take >> a >> while >> WARN: >> It >> is >> recommended >> to >> run >> this >> step >> on >> a >> cluster >> bedpostx_mgh >> -n >> 2 >> /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri >> /usr/local/freesurfer/bin/bedpostx_mgh: >> 131: >> /usr/local/freesurfer/bin/bedpostx_mgh: >> Syntax >> error: >> "(" >> unexpected >> http://www1.imperial.ac.uk/medicine/people/d.soto/ >> >> ________________________________________ >> From: >> Anastasia >> Yendiki >> [ayendiki(a)nmr.mgh.harvard.edu] >> Sent: >> 07 >> August >> 2013 >> 17:22 >> To: >> Soto, >> David >> Cc: >> freesurfer(a)nmr.mgh.harvard.edu >> Subject: >> RE: >> [Freesurfer] >> trac-all >> inquiry >> >> Hi >> David >> - >> Every >> time >> you >> run >> trac-all, >> the >> results >> get >> appended >> to >> this >> file, >> so >> you >> need >> to >> look >> for >> error >> messages >> only >> in >> the >> more >> recent >> invocation >> of >> trac-all. >> The >> first >> error >> there >> seems >> to >> be: >> >> >> Error: >> bvecs >> and >> bvals >> don't >> have >> the >> same >> number >> of >> entries >> >> Do >> you >> have >> the >> same >> number >> of >> b-values >> and >> gradient >> vectors >> and >> volumes >> in >> your >> DWI >> series? >> >> a.y >> >> On >> Tue, >> 6 >> Aug >> 2013, >> Soto, >> David >> wrote: >> >> hi >> >> I >> upgraded >> to >> FS >> 5.3 >> but >> still >> encountering >> issues >> with >> trac-all >> prep. >> >> The >> log >> is >> attached, >> things >> I >> noted >> after >> inspecting >> it >> >> 1) >> INFO: >> FreeSurfer >> build >> stamps >> do >> not >> match >> Subject >> Stamp: >> freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 >> Current >> Stamp: >> freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 >> >> 2) >> Error: >> input >> image >> /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/lowb >> not >> valid >> 3) >> Image >> Exception >> : >> #22 >> :: >> ERROR: >> Could >> not >> open >> image >> /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/lowb_brain >> 4) >> Image >> Exception >> : >> #22 >> :: >> ERROR: >> Could >> not >> open >> image >> /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/diff/White-Matter++. >> 5) >> ERROR: >> Could >> not >> read >> /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/dtifit_FA.nii.gz >> but >> despite >> all >> this >> it >> says: >> trac-preproc >> finished >> without >> error >> at >> Tue >> Aug >> 6 >> 21:27:30 >> BST >> 2013 >> >> thanks >> for >> your >> help >> >> cheers >> ds >> >> http://www1.imperial.ac.uk/medicine/people/d.soto/ >> >> >> >> >> ________________________________________ >> From: >> Anastasia >> Yendiki >> [ayendiki(a)nmr.mgh.harvard.edu] >> Sent: >> 06 >> August >> 2013 >> 19:30 >> To: >> Soto, >> David >> Cc: >> freesurfer(a)nmr.mgh.harvard.edu >> Subject: >> RE: >> [Freesurfer] >> trac-all >> inquiry >> >> I >> see, >> you're >> using >> the >> old >> version >> of >> tracula >> (from >> freesurfer >> 5.1). >> In >> that >> version, >> you >> had >> to >> define >> the >> number >> of >> low-b >> images >> in >> the >> configuration >> file. >> I >> strongly >> recommend >> updating >> to >> freesurfer >> 5.3. >> A >> lot >> of >> things >> have >> improved >> in >> tracula >> since >> then. >> >> Also, >> in >> the >> future >> please >> attach >> any >> log >> files >> as >> separate >> attachments >> instead >> of >> pasting >> them >> into >> the >> body >> of >> your >> email >> - >> this >> causes >> the >> body >> of >> the >> email >> to >> exceed >> the >> limit >> allowable >> on >> the >> list. >> >> Thanks, >> a.y >> >> >> 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] Setting up enviornment variable permenantly
by Bruce Fischl 11 Aug '13

11 Aug '13

can you cc the list so that others can help? Have you looked for the file: ~/.tchsrc it won't show up in ls unless you specify the -a option (all I think) as the dot files are hidden by default. Bruce On Sun, 11 Aug 2013, Muhammad Naveed Iqbal Qureshi wrote: > Hi, I am using Ubuntu 12.04 and using tcsh computer specs are core i7 3.6ghz with 32 gb ram > > Thank you > > Best Regards, > Muhammad Naveed Iqbal Qureshi > > On 11-Aug-2013, at 10:20 PM, "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> wrote: > >> Hi Naveed >> >> what kind of computer are you using? The .cshrc would be in your home directory. Do you know what shell you are running? >> Bruce >> >> >> On Sun, 11 Aug 2013, Muhammad Naveed Iqbal Qureshi wrote: >> >>> Hello, >>> >>> I am unable to find the .tcshrc files. Where can I find it. >>> >>> I am unable to follow this process as stated on the website. >>> >>> Alternately, the resource file for the shell can be configured to source the >>> file automatically each time the shell is started. In the home directory of >>> the user who will be running FreeSurfer binaries, edit the file .cshrc if >>> C-shell will be used, the .tcshrc for enhanced C-shell, the .bashrc file for >>> Bash, and .profile for sh, to include the previous two lines (which setenv >>> FREESURFER_HOME, and then source the SetUpFreeSurfer.csh(or sh) script). >>> >>> Best Regards, >>> Naveed >>> >>> >> >> >> 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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surface to volume
by Fernando Valle-Inclán 11 Aug '13

11 Aug '13

Hi freesurfers, Is it possible to transform the statistical results of a surface analysis into an anatomical volumen? I've been reading about tkregister2 and mri_surf2vol, but I'm not confident. Any help would be appreciated Fernando Valle-Inclan

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Setting up enviornment variable permenantly
by Muhammad Naveed Iqbal Qureshi 11 Aug '13

11 Aug '13

Hello, I am unable to find the .tcshrc files. Where can I find it. I am unable to follow this process as stated on the website. Alternately, the resource file for the shell can be configured to source the file automatically each time the shell is started. In the home directory of the user who will be running FreeSurfer binaries, edit the file .cshrc if C-shell will be used, the .tcshrc for enhanced C-shell, the .bashrc file for Bash, and .profile for sh, to include the previous two lines (which setenv FREESURFER_HOME, and then source the SetUpFreeSurfer.csh(or sh) script). Best Regards, Naveed

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Re: [Freesurfer] nu.mgz intensity too dark
by Bruce Fischl 09 Aug '13

09 Aug '13

Hi Abid you can run recon-all -make all -s .... and that should do it (since the timestamp on the orig has changed) cheers Bruce On Fri, 9 Aug 2013, Abid Qureshi wrote: > Hi Dr. Fischl, > I've changed the intensity on the orig.mgz files so that there is better > differentiation between white matter and gray matter. Then do I restart > recon-all after a certain step in the process? How does recon-all know to > use the newly modified orig.mgz file. > > Thanks, > Abid > > > On Thu, Aug 8, 2013 at 9:54 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > wrote: > Hi Abid > > --scale specifies a floating point number to multiply each voxel > intensity by, so --scale 0.5 will make every intensity half as > much > > cheers > Bruce > > > On Thu, 8 Aug 2013, aqureshi(a)nmr.mgh.harvard.edu wrote: > > When I looked at orig.mgz it is actually too bright. It's > very hard to > differentiate white and gray matter from how bright the > image is. Maybe > that is the root of the problem. I tried correcting it > with mri_convert > like this: > > cp orig.mgz holder_orig.mgz > mri_convert --scale 3 holder_orig.mgz orig.mgz > > But scale 2-5 all increase the brightness further, which > would probably > worsen the problem. I wasn't able to find how to decrease > brightness (or > increase contrast) in mri_convert --help. How would I > decrease the > brightness? It does not take negative numbers (like -3). > > Thanks, > Abid > > > > ------------------ > > maybe try scaling up the orig.mgz then? I never really > understood why the > nu darkens it sometime. Alternatively you could scale up > the nu, but you > will have already lost dynamic range > > ------------------ > > The 001.mgz actually looks good in this case > (in terms of intensity) so > I'm not sure if it makes sense to scale it up > further. The problem is with > the nu.mgz being too dark. I'll try it out > though if you think it will > also work in this case. > > - Abid > > > --------------- > > you could try using --scale <scale factor> to > scale the intensities of the > 001.mgz up > > --------------- > > Hi Dr. Fischl, > > I had a couple subjects that > failed recon-all. Although the > error log > said > recon-all failed at mri_watershed > it looks like the root problem is > a > couple steps earlier, because the > nu.mgz looks too dark. This was > discussed in a previous thread > from 2008. > > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07293.html. > > You wrote, "p.s. are the 001.mgz > and 002.mgz dark? The orig.mgz? > Sometimes > nu_correct can create very dark > images, and there are some > switches you > can loo through to correct them. > Alternatively if it is the > 001.mgz, > mri_convert has a scale option you > can use." > > On my subject 001.mgz looks good > (there was no 002.mgz file). It is > only > nu.mgz that looks too dark. It > looks like the solution you gave > then was > for a problematic 001.mgz file, > but from your response it looks as > if > the > problem was nu.mgz the solution > would be different. What are the > switches > you can loop through to correct > the nu.mgz. > > Thanks, > Abid > > > > > > > > > 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. > > > > > -- > WARNING: E-mail sent over the Internet is not secure. Information sent by > e-mail may not remain confidential. > > DISCLAIMER: This e-mail is intended only for the individual to whom it is > addressed. It may be used only in accordance with applicable laws. If you > received this e-mail by mistake, notify the sender and destroy the e-mail > >

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