Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30096 discussions

Some Questions Regarding W Files
by Zhongtian Dai 27 Jun '13

27 Jun '13

Hi, I want to ask some questions about w files: 1. does Freeview read and display w files? (if not, any plan to support it?) 2. does tksurfer support custom color scale? how to change a color scale's bounds? they seem to change with overlay's min and max but not consistently. 3. does anything resembling a multi-frame w file exist? Cheers, -- Zhongtian (Falcon) Dai B.S. with Honors in Mathematics & B.A. with Honors in Physics University of Chicago 2012 web <http://falcondai.com/> | blog <http://blog.falcondai.com/> | g+<https://plus.google.com/100753323689686892506> | twitter <https://twitter.com/falcondai> | github<https://github.com/falcondai> | weibo <http://www.weibo.com/falcondai>

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Re: [Freesurfer] freesurfer registration
by Martin Reuter 27 Jun '13

27 Jun '13

Hi Chris, for the motion correction step there is no bias-field correction. First it is assumed that bias field is not very different (scans are from the same session) and also the robust register can down-weigh regions that differ a lot. However the methods estimates a global intensity scale parameter simultaneously during the registration to adjust intensity values across the images (that's in the robust register paper). Best, Martin On 06/27/2013 06:45 AM, Parker, Christopher wrote: > Hi Martin, > > Are the images bias-field corrected before registration in recon-all? > If so, which method is used for this? Is there a paper for > reference/citation also? > > Many Thanks, > Chris > ------------------------------------------------------------------------ > *From:* Martin Reuter [mreuter(a)nmr.mgh.harvard.edu] > *Sent:* 25 June 2013 18:53 > *To:* Bruce Fischl > *Cc:* Parker, Christopher; freesurfer(a)nmr.mgh.harvard.edu > *Subject:* Re: [Freesurfer] freesurfer registration > > Hi Chris, > > we actually do use my robust registration tool for it since a while > (FS 5.0, Aug 2010), replacing FLIRT which was used before. Here is the > citation: > > M. Reuter, H.D. Rosas, B. Fischl. *Highly Accurate Inverse Consistent > Registration: A Robust Approach*. /NeuroImage 53(4):1181-1196, 2010/. > > It is a robust rigid registration, using the tukey biweight function > on the residuals. The statistical robustness makes it less sensitive > to outliers (e.g. differences in jaw, neck, eye regions) by > identifying regions with local differences during the registration and > reducing their influence on the registration. This leads to very > accurate alignment in the regions that do not change (the brain). > > Cheers, Martin > > On 06/25/2013 12:05 PM, Bruce Fischl wrote: >> yes, it's rigid and used to be sum of squares but in the newer versions we >> will be using Martin's robust registration (which is a tukey biweight >> instead of SSE) >> >> On Tue, 25 Jun 2013, Parker, Christopher wrote: >> >>> Hi, >>> I understand that the recon-all script registers and then averages two >>> anatomical images (after bias field correction) if two are provided in the >>> "orig" folder, before performing the other parcellation stages. I am writing >>> a report and it might be good to mentioned what registration is used. I'm >>> guessing this is a rigid registration using sum of squared differences cost >>> function? >>> >>> Best, >>> Chris >>> >>> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > > -- > Martin Reuter, Ph.D. > Assistant in Neuroscience - Massachusetts General Hospital > Instructor in Neurology - Harvard Medical School > MGH / HMS / MIT > > A.A.Martinos Center for Biomedical Imaging > 149 Thirteenth Street, Suite 2301 > Charlestown, MA 02129 > > Phone: +1-617-724-5652 > Email: > mreuter(a)nmr.mgh.harvard.edu > reuter(a)mit.edu > Web :http://reuter.mit.edu > > 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. > -- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreuter(a)nmr.mgh.harvard.edu reuter(a)mit.edu Web : http://reuter.mit.edu

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further description of 'mris_divide_parcellation' for high resolution atlas of the cortex
by Montillo, Albert (GE Global Research) 27 Jun '13

27 Jun '13

Does anyone have further documentation on 'mris_divide_parcellation' ? Is there a picture of what it does? It is referred to in the FreeSurfer FAQ Q. How can I get a high resolution atlas of the cortex in Freesurfer? A: This can be accomplished using 'mris_divide_parcellation'. You can pass your preferred max area of a parcellation and it will keep subdividing along the primary eigen-axis until no units are above that surface area.

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Bad resolution of recon-all -autorecon1
by ye tian 27 Jun '13

27 Jun '13

Dear freesurfers, After executing recon-all with -autorecon1, I opened the image Barba50527_2 *T1.mgz* from tkmedit. The bad resolution leads me to doubt that my input format wasn't correct. I input two sequences of images. Each image resembles the attachment Sample Input. There are 439 such image in each sequence. Would you please shine some light on my bad resolution? Thank you very much! Sincerely, Ye

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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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