Freesurfer

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30132 discussions

cortical parcellation: atlas modification and speed/accuracy trade-off
by Montillo, Albert (GE Global Research) 27 Jun '13

27 Jun '13

At times, I would like to use FreeSurfer to just produce cortical parcellation and do not need other results like subcortical parcellation and cortical thickness. How can I run the bare minimum number of steps to generate the cortical parcellation labeled volume? (Does anyone have a script that runs just these steps?) Similarly if I want to speed cortical parcellation and can accept lower accuracy as a tradeoff, are there parameters I can set to enable such a speed/accuracy tradeoff? Now on the flip-side, for other subjects I would like to change the granularity of the cortical parcels that FreeSurfer uses, to use finer parcels. How do I construct a new cortical parcellation atlas with more labels? Best, Albert

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How are time point exclude files used in FSFAST?
by Caspar M. Schwiedrzik 26 Jun '13

26 Jun '13

Hi Freesurfer experts, I was wondering how exactly time point exclude files are used by FSFAST. Are the time points removed from the time series before the GLM, or is the time point exclude file used to build a nuisance predictor (as in FSL's motion outliers routine, http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSLMotionOutliers)? If the time points are removed from the time series, how is that accounted for when calculating the autocorrelation for the whitening / during (high pass) filtering? Thanks, Caspar

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creating an entorhinal cortex volume from ?h.entorhinal_exvivo.label
by Mehul Sampat 26 Jun '13

26 Jun '13

Hi Folks, I am trying to create an entorhinal cortex volume from ?h.entorhinal_exvivo.label using mri_label2vol I cd to the subject dir ($SUBJECTS_DIR/bert) and the command I use is: *mri_label2vol --label label/lh.entorhinal_exvivo.label --temp mri/nu.mgz --identity --o mri/lh-new-erc.mgz * I took the sum of the voxels in this new mask i created (lh-new-erc.mgz) and it is 215; I looked at the volume provided in lh.entorhinal_exvivo.stats and it is 925; (from the log file I believe this is created using the command: mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b -l ./lh.entorhinal_exvivo.label bert lh white) I was expecting the numbers to match or at-least be close; I am guessing I am using mri_label2vol incorrectly ? Could someone help me with this issue ? Thanks Mehul

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Inputs to recon-all -i
by ye tian 26 Jun '13

26 Jun '13

Dear freesurfers, I have a general question concerning *recon-all -i*. Suppose under the subject *Beth*, there are 256 files: Beth1.1.ima, Beth1.2.ima, Beth1.3.ima, ..., Beth1.128.ima Beth2.1.ima, Beth2.2.ima, Beth2.3.ima, ..., Beth2.128.ima I understand that I can use the following command to import the data *recon-all -s Beth -i /Path_to_Beth/Beth1.1.ima* * -i /Path_to_Beth/Beth2.1.ima* which gives 001.mgz and 002.mgz in the Beth/mri/orig/ Now what if I rename the sequence as follows, Beth2.1.ima -----> Beth1.129.ima Beth2.2.ima -----> Beth1.130.ima ...... Beth2.128.ima -----> Beth1.256.ima and import using *recon-all -s Beth -i /Path_to_Beth/Beth1.1.ima, *leading to 001.mgz alone. Would it make a difference? Thank you very much! Sincerely, Ye

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Re: [Freesurfer] pvr help
by Gautam, Prapti 26 Jun '13

26 Jun '13

Hi Doug, This is the complete terminal output: cwd /SA cmdline mri_glmfit --y /FREESURFER/lh.thickness.15.mgh --fsgd SA_base.fsgd --C /FREESURFER/con4.mtx --surf fsaverage lh --cortex --glmdir /FREESURFER/lh.pair-thick-T1-00.glmdir --pvr /FREESURFER/lh.paired-cope1.psc.00.mgh sysname Linux hostname einstein machine x86_64 user pgautam FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /FREESURFER/lh.thickness.15.mgh logyflag 0 usedti 0 FSGD SA_base.fsgd labelmask /fsaverage/label/lh.cortex.label maskinv 0 glmdir /FREESURFER/lh.pair-thick-T1-00.glmdir IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory /FREESURFER/lh.pair-thick-T1-00.glmdir Loading y from /FREESURFER/lh.thickness.15.mgh INFO: gd2mtx_method is dods Saving design matrix to /FREESURFER/lh.pair-thick-T1-00.glmdir/Xg.dat Normalized matrix condition is 1.30805 Matrix condition is 6.34773 Found 149955 points in label. Pruning voxels by thr: 0.000000 Found 149953 voxels in mask Saving mask to /FREESURFER/lh.pair-thick-T1-00.glmdir/mask.mgh Reshaping mriglm->mask... search space = 74612.446501 DOF = 54 Starting fit and test Matrix is Ill-conditioned 1.000 0.000 1.029 0.000 0.000; 1.000 0.000 0.838 0.000 0.000; 1.000 0.000 0.318 0.000 0.000; 1.000 0.000 0.561 0.000 0.000; 1.000 0.000 0.622 0.000 0.000; 1.000 0.000 0.882 0.000 0.000; 1.000 0.000 2.059 0.000 0.000; 1.000 0.000 0.945 0.000 0.000; 1.000 0.000 1.090 0.000 0.000; 1.000 0.000 1.245 0.000 0.000; 1.000 0.000 0.571 0.000 0.000; 1.000 0.000 0.337 0.000 0.000; 1.000 0.000 1.105 0.000 0.000; 1.000 0.000 0.990 0.000 0.000; 1.000 0.000 1.074 0.000 0.000; 1.000 0.000 1.552 0.000 0.000; 1.000 0.000 1.020 0.000 0.000; 1.000 0.000 0.829 0.000 0.000; 1.000 0.000 0.522 0.000 0.000; 1.000 0.000 1.152 0.000 0.000; 1.000 0.000 0.429 0.000 0.000; 1.000 0.000 1.003 0.000 0.000; 1.000 0.000 0.515 0.000 0.000; 1.000 0.000 1.500 0.000 0.000; 1.000 0.000 -4.639 0.000 0.000; 1.000 0.000 -5.227 0.000 0.000; 1.000 0.000 -5.051 0.000 0.000; 1.000 0.000 -4.918 0.000 0.000; 1.000 0.000 -5.316 0.000 0.000; 1.000 0.000 -5.311 0.000 0.000; 0.000 1.000 0.000 2.172 0.000; 0.000 1.000 0.000 1.115 0.000; 0.000 1.000 0.000 1.056 0.000; 0.000 1.000 0.000 1.372 0.000; 0.000 1.000 0.000 1.267 0.000; 0.000 1.000 0.000 0.847 0.000; 0.000 1.000 0.000 0.682 0.000; 0.000 1.000 0.000 0.524 0.000; 0.000 1.000 0.000 0.682 0.000; 0.000 1.000 0.000 0.930 0.000; 0.000 1.000 0.000 0.126 0.000; 0.000 1.000 0.000 1.113 0.000; 0.000 1.000 0.000 1.066 0.000; 0.000 1.000 0.000 0.517 0.000; 0.000 1.000 0.000 0.598 0.000; 0.000 1.000 0.000 2.061 0.000; 0.000 1.000 0.000 2.003 0.000; 0.000 1.000 0.000 1.204 0.000; 0.000 1.000 0.000 0.975 0.000; 0.000 1.000 0.000 1.445 0.000; 0.000 1.000 0.000 1.327 0.000; 0.000 1.000 0.000 1.731 0.000; 0.000 1.000 0.000 1.610 0.000; 0.000 1.000 0.000 1.145 0.000; 0.000 1.000 0.000 0.102 0.000; 0.000 1.000 0.000 -4.364 0.000; 0.000 1.000 0.000 -5.073 0.000; 0.000 1.000 0.000 -4.607 0.000; 0.000 1.000 0.000 -5.355 0.000; Matrix is Ill-conditioned .. ------------------------------ Message: 8 Date: Thu, 13 Jun 2013 13:21:00 -0400 From: Douglas Greve <greve(a)nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] pvr help To: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Message-ID: <51B9FF7C.7020200(a)nmr.mgh.harvard.edu<mailto:51B9FF7C.7020200@nmr.mgh.harvard.edu>> Content-Type: text/plain; charset="iso-8859-1" Hi Prapti, can you send the full terminal output? The ill-conditioned error is probably not related to the contrast. It is usually related to the design matrix, which makes it difficult to track down because you will have a different one at each vertex with --pvr. doug On 6/13/13 1:14 PM, Gautam, Prapti wrote: Dear FreeSurfers I am trying to control for thickness in another surface using the pvr option in mri_glmfit. However, I'm confused as to how I can include the pvr option correctly in the contrast files. I have two groups, and would like to utilize DODS for this analyses as I think that my groups both have different intercepts and slopes. This is my fsgd set up : GroupDescriptorFile1 TitleMyTitle ClassControls CLASS FA VariablesAge InputPMS1Controls14.442163 InputPMS2Controls14.354552 .. InputPMS7FA15.726215 InputPMS28FA14.45859 This is the command I run: mri_glmfit --y lh.surface.mgh --fsgd SA_age.fsgd --C con.mtx --surf fsaverage lh --cortex --glmdir test.glmdir --pvr lh.thickness.psc.mgh --pvr lh.thickness2.psc.mgh The contrast I would like to run is: 0 0 0 0 1 -1 so as to look at group interactions within thickness after controlling for another cortical surface. However, I can't get this to run as there is a "Matrix ill-conditioned" error. The contrast that does run is 0 0 0 0 1 (after passing only one pvr file). But this option seems to be neither dods nor doss. Is there a correct way to do a DODS analyses looking for interactions using the pvr option? Thank you, Prapti --------------------------------------------------------------------- CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential or legally privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of this original message. ---------------------------------------------------------------------

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Re: [Freesurfer] Multiple frame error with recon-all
by ye tian 26 Jun '13

26 Jun '13

Dear FreeSurfers, Sorry I accidentally clicked "send" before I finished. I will send a new link. Would the moderator please delete the previous link? Sorry! Ye On Wed, Jun 26, 2013 at 5:34 PM, ye tian <tianye730(a)gmail.com> wrote: > Dear FreeSurfers, > > Recon-all exits with the following error > > *ERROR: input(s) cannot have multiple frames!* > *$SUBJECTS_DIR/Barba50527_2/mri/orig/001.mgz has 439 frames* > > If I open 001.mgz using freeview, I obtain the image in the attachment > saved as *freeview 001.mgz.png*. > > > In order to make sure that my problem does not come from further upstream, > I am including the major steps that I took to get to this error. > > *STEP0*: > My inherited data has names > BARBA50527.MR.MEDITATE_MEDITATION.*#*.*#*.year.month.day.#.#.#.#.#.IMA > where each # is a string of numbers. > > > *STEP1*: > The images can be grouped into five categories, according to the numbers > in the names that occupy the positions of the red #: 1.1-1.3, 2.1, > 3.1-3.160, 4.1-4.439, 5.1-5.439 > > [1] Note: Images from groups 4 & 5 are very different from the images of > groups 1, 2 and 3. An example of each is included in the attachment. >

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Re: [Freesurfer] Multiple frame error with recon-all
by ye tian 26 Jun '13

26 Jun '13

Hello Bruce, Sorry! The first email was too big and the mailing list rejected me. My image was already in Jpeg though. Sincerely, Ye On Wed, Jun 26, 2013 at 5:17 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > Hi Ye, > > can you cc the list so that others can help you? 787 would usually be too > many files for an anatomical. Something on the order of 170-256 is more > typical. If you visualize them the white matter should be bright, the gray > matter darker and the CSF very dark > > > Bruce > > > On Wed, 26 Jun 2013, ye tian wrote: > > Dear Bruce, >> I just confirmed a few hours ago that I indeed have structural MRI data >> though. I have attached an example of the last 787 files from my data >> below. >> In fact, I tried to use only those to reconstruct my volumes and surfaces. >> >> Do they serve as inputs to freesurfer? >> >> Thank you very much! >> >> Sincerely, >> Ye >> >> >> On Wed, Jun 26, 2013 at 5:04 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu >> > >> wrote: >> no, once they have been acquired you can't change anything. You >> have to hope that they also acquired structural data in addition >> to the functional data (which is quite common). You can't change >> the way your images were formed posthoc... >> >> On Wed, 26 Jun 2013, ye tian wrote: >> >> Dear Bruce, >> If I understand correctly, I should bring these >> images back to the scanner >> and change some settings. Am I right? >> >> Sincerely, >> Ye >> >> >> On Wed, Jun 26, 2013 at 4:59 PM, Bruce Fischl >> <fischl(a)nmr.mgh.harvard.edu> >> wrote: >> you need to know what different scan types >> were acquired. The >> ones you showed were the fMRI time-series and >> designed to >> hilight changes in blood oxygenation level, >> which is an indirect >> marker of changes in neural firing, not >> anatomy >> >> On Wed, 26 Jun 2013, ye tian wrote: >> >> Dear Bruce, >> I inherited the data from a previous >> graduate >> student. I sent out a message >> to learn more information about the >> scanner a few >> days ago. >> What information do I need to know about >> the >> scanner? >> >> Thank you so much for your time and >> effort! >> >> Sincerely, >> Ye >> >> >> On Wed, Jun 26, 2013 at 4:41 PM, Bruce >> Fischl >> <fischl(a)nmr.mgh.harvard.edu> >> wrote: >> Hi Ye >> >> you can't convert it, you have to >> acquire it >> that way. Where did >> you get your data? >> >> Bruce >> On Wed, 26 Jun 2013, ye tian >> wrote: >> >> Dear Bruce, >> Sorry for my lack of >> knowledge. I looked >> online, but >> couldn't find how to >> convert MRI data to >> T1-weighted >> anatomical. Would >> you please shine some >> light on it? >> >> Thank you very much! >> >> Sincerely, >> Ye >> >> >> On Wed, Jun 26, 2013 at 4:21 >> PM, Bruce >> Fischl >> <fischl(a)nmr.mgh.harvard.edu> >> wrote: >> Hi Ye >> >> you need to give >> recon-all a >> T1-weighted >> anatomical (e.g. >> mprage, SPGR/FLASH, >> etc...), not >> the fMRI >> data. >> >> cheers >> Bruce >> On Wed, 26 Jun 2013, >> ye tian >> wrote: >> >> Dear Bruce, >> >> Recon-all exits >> with the >> following error >> >> ERROR: input(s) >> cannot have >> multiple >> frames! >> >> >> >> $SUBJECTS_DIR/Barba50527_2/**mri/orig/001.mgz has 439 >> frames >> >> If I open >> 001.mgz using >> freeview, I >> obtain the image >> in the >> attachment saved >> as freeview >> 001.mgz.png. >> >> >> >> In order to make >> sure that >> my problem >> does not come >> from further >> upstream, I >> am including the >> major steps >> that I took >> to get to >> this error. >> >> MAJOR STEPS >> >> STEP0: >> My inherited >> data has names >> >> >> >> BARBA50527.MR.MEDITATE_**MEDITATION.#.#.year.month.day.** >> #.#.#.#.#.IMA >> where each # is >> a string of >> numbers. >> >> >> STEP1: >> The images can >> be grouped >> into five >> categories, >> according to the >> numbers in >> the names that >> occupy the >> positions of >> the red #: >> 1.1-1.3, >> 2.1, >> 3.1-3.160, >> 4.1-4.439, >> 5.1-5.439 >> >> [1] Note: Images >> from groups >> 4 & 5 are >> very >> different from >> the images of >> groups 1, 2 and >> 3. A link to >> a youtube >> video of all >> the images can >> be seen >> in note[1]. >> >> >> STEP2: >> recon-all -s >> Barba50527_2 >> -i >> >> >> >> /Path_to_data/BARBA50527.MR.**MEDITATE_MEDITATION.4.1.2010.** >> 07.27.10.52.51 >> >> .437500.56148038.IMA >> -i >> >> >> >> /Path_to_data/BARBA50527.MR.**MEDITATE_MEDITATION.5.1.2010.** >> 07.27.10.52.51 >> >> .437500.56148502.IMA >> recon-all >> completes without >> error. >> >> [2] Note: other >> attempts >> leads to >> different errors. >> See note [2] for >> details. >> >> >> STEP3: >> recon-all -s >> Barba50527_2 >> -autorecon1 >> >> Exits with the >> error message >> at the >> beginning of the >> email. The >> number 439 >> seems to come >> from the >> number of files >> in each >> group. >> >> >> USEFUL COMMENTS >> >> >> >> >> http://www.mail-archive.com/**freesurfer@nmr.mgh.harvard.** >> edu/msg23764.html<http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23764.html> >> >> I will do it for >> 001.mgz and >> 002.mgz and >> will let >> you know how it >> goes. >> >> >> QUESTIONS >> 1. Do I really >> need to >> manually parse >> the sequence >> of images? If >> so, how? >> 2. I don't >> really need to >> mri_convert my >> files into >> other formats, >> e.g., >> .dcm, do I? >> 3. Each file >> from groups 4 >> and 5 have >> multiple >> images. Do I >> need to cut >> them >> into sub-images, >> each with >> one brain? >> >> Thank you very >> much! >> >> Sincerely, >> Ye >> >> >> >> >> >> NOTES: >> Note [1] >> A video of the >> data can be >> found at >> >> >> >> http://www.youtube.com/watch?**v=W8ZFGvGvHVc&list=** >> UUfGdQq3j1gqPAc4z6Spmu2g<http://www.youtube.com/watch?v=W8ZFGvGvHVc&list=UUfGdQq3j1gqPAc4z6Spmu2g> >> >> On the top left >> corner: >> the white text >> is: >> current frame >> number / total >> frame number >> the yellow text >> is: the >> name of the >> frame >> >> Note[2] >> recon-all -s >> Barba50527_2 >> -i >> >> >> >> /Path_to_data/BARBA50527.MR.**MEDITATE_MEDITATION.1.1.2010.** >> 07.27.10.52.51 >> >> .437500.56141898.IMA >> Completes >> without error >> recon-all -s >> Barba50527_2 >> -autorecon1 >> Warning: only >> one run found >> Error: >> MRIsample(): source >> matrix has >> zero >> determinant; >> matrix is: >> EOF >> >> econ-all -s >> Barba50527_2 >> -i >> >> >> >> /Path_to_data/BARBA50527.MR.**MEDITATE_MEDITATION.1.1.2010.** >> 07.27.10.52.51 >> >> .437500.56141898.IMA >> -i >> >> >> >> /Path_to_data/BARBA50527.MR.**MEDITATE_MEDITATION.2.1.2010.** >> 07.27.10.52.51 >> >> .437500.56148502.IMA >> -i >> >> >> >> /Path_to_data/BARBA50527.MR.**MEDITATE_MEDITATION.3.1.2010.** >> 07.27.10.52.51 >> >> .437500.56148502.IMA >> -i >> >> >> >> /Path_to_data/BARBA50527.MR.**MEDITATE_MEDITATION.4.1.2010.** >> 07.27.10.52.51 >> >> .437500.56148038.IMA >> -i >> >> >> >> /Path_to_data/BARBA50527.MR.**MEDITATE_MEDITATION.5.1.2010.** >> 07.27.10.52.51 >> >> .437500.56148502.IMA >> error.log: >> matrix >> dimensionality >> >> >> >> >> >> 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>. >> 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] Multiple frame error with recon-all
by Bruce Fischl 26 Jun '13

26 Jun '13

Hi Ye you need to give recon-all a T1-weighted anatomical (e.g. mprage, SPGR/FLASH, etc...), not the fMRI data. cheers Bruce On Wed, 26 Jun 2013, ye tian wrote: > Dear Bruce, > > Recon-all exits with the following error > > ERROR: input(s) cannot have multiple frames! > $SUBJECTS_DIR/Barba50527_2/mri/orig/001.mgz has 439 frames > > If I open 001.mgz using freeview, I obtain the image in the attachment saved > as freeview 001.mgz.png. > > > > In order to make sure that my problem does not come from further upstream, I > am including the major steps that I took to get to this error. > > MAJOR STEPS > > STEP0: > My inherited data has names > BARBA50527.MR.MEDITATE_MEDITATION.#.#.year.month.day.#.#.#.#.#.IMA > where each # is a string of numbers. > > > STEP1: > The images can be grouped into five categories, according to the numbers in > the names that occupy the positions of the red #: 1.1-1.3, 2.1, > 3.1-3.160, 4.1-4.439, 5.1-5.439 > > [1] Note: Images from groups 4 & 5 are very different from the images of > groups 1, 2 and 3. A link to a youtube video of all the images can be seen > in note[1]. > > > STEP2: > recon-all -s Barba50527_2 > -i > /Path_to_data/BARBA50527.MR.MEDITATE_MEDITATION.4.1.2010.07.27.10.52.51 > .437500.56148038.IMA > -i > /Path_to_data/BARBA50527.MR.MEDITATE_MEDITATION.5.1.2010.07.27.10.52.51 > .437500.56148502.IMA > recon-all completes without error. > > [2] Note: other attempts leads to different errors. See note [2] for > details. > > > STEP3: > recon-all -s Barba50527_2 -autorecon1 > > Exits with the error message at the beginning of the email. The number 439 > seems to come from the number of files in each group. > > > USEFUL COMMENTS > > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23764.html > > I will do it for 001.mgz and 002.mgz and will let you know how it goes. > > > QUESTIONS > 1. Do I really need to manually parse the sequence of images? If so, how? > 2. I don't really need to mri_convert my files into other formats, e.g., > .dcm, do I? > 3. Each file from groups 4 and 5 have multiple images. Do I need to cut them > into sub-images, each with one brain? > > Thank you very much! > > Sincerely, > Ye > > > > > > NOTES: > Note [1] > A video of the data can be found at > http://www.youtube.com/watch?v=W8ZFGvGvHVc&list=UUfGdQq3j1gqPAc4z6Spmu2g > > On the top left corner: > the white text is: current frame number / total frame number > the yellow text is: the name of the frame > > Note[2] > recon-all -s Barba50527_2 > -i > /Path_to_data/BARBA50527.MR.MEDITATE_MEDITATION.1.1.2010.07.27.10.52.51 > .437500.56141898.IMA > Completes without error > recon-all -s Barba50527_2 -autorecon1 > Warning: only one run found > Error: MRIsample(): source matrix has zero determinant; matrix is: EOF > > econ-all -s Barba50527_2 > -i > /Path_to_data/BARBA50527.MR.MEDITATE_MEDITATION.1.1.2010.07.27.10.52.51 > .437500.56141898.IMA > -i > /Path_to_data/BARBA50527.MR.MEDITATE_MEDITATION.2.1.2010.07.27.10.52.51 > .437500.56148502.IMA > -i > /Path_to_data/BARBA50527.MR.MEDITATE_MEDITATION.3.1.2010.07.27.10.52.51 > .437500.56148502.IMA > -i > /Path_to_data/BARBA50527.MR.MEDITATE_MEDITATION.4.1.2010.07.27.10.52.51 > .437500.56148038.IMA > -i > /Path_to_data/BARBA50527.MR.MEDITATE_MEDITATION.5.1.2010.07.27.10.52.51 > .437500.56148502.IMA > error.log: matrix dimensionality > > >

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libboost_program_options.so.5 issue
by Hoptman, Matthew 26 Jun '13

26 Jun '13

Hi all, Any news on the libboost_program_options.so.5 issue, as relates to mri_cvs_register? I've encountered it using mris_resample (as part of mri_cvs_register) using. When I run: qsub -S /bin/tcsh -pe make 2 -b y -v PATH=${FREESURFER_HOME}/bin:$PATH -V ${FREESURFER_HOME}/bin/mri_cvs_register --mov ${subject} where ${subject} was found by looping through all of my subjects I get the error: mris_resample: error while loading shared libraries: libboost_program_options.so.5: cannot open shared object file: No such file or directory bugr gives me: ---------------------------------------------------------------- FREESURFER_HOME: /home/hoptman/freesurfer Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0beta Debian version: 6.0.4 Kernel info: Linux 2.6.32-5-amd64 x86_64 Thanks, Matt Matthew J. Hoptman, PhD Research Scientist V Nathan S. Kline Institute for Psychiatric Research Research Associate Professor in Psychiatry NYU School of Medicine IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. ________________________________ Conserve Resources. Print only when necessary. IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation.

1 1

Substantia Nigra
by Ata Akh 26 Jun '13

26 Jun '13

Hello Dear Freesurfers, is there a possibility, a way, to visualize the substantia nigra in Freesurfer like using 3DSlicer!? Thanks Ata

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