Freesurfer

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30132 discussions

temporal lobe cut off
by Gibbard, Clare 12 Jan '12

12 Jan '12

Hi, I ran recon-all -all -subjid subjectx on around 40 scans. The registrations and skull strips look fine. However, the white matter and pial surface segmentations miss out the left anterior temporal lobe in most subjects. I tried adding in control points to the left temporal lobe and running recon-all -autorecon2-cp -autorecon3 -subjid subjectx. This helped to fill in the missing areas, but new parts of the right temporal lobe were cut out. I then tried adding in control points to both the left and right temporal lobes, but again new regions of the left temporal lobe were cut out. I think it must be an intensity issue, but I can't see how to fix it. Are you able to give me a work flow to sort this? Here are some screenshots: [X][X]Before control points added: [cid:3abaf95b-5c72-4441-9e12-40d1fd13f01c] After control points added to left and right temporal lobes: [cid:e76a0d57-608a-449a-b7b1-e927de878bda] Thank you. Best wishes, Clare Gibbard

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Re: [Freesurfer] Non_FA Group study
by Antonella Kis 12 Jan '12

12 Jan '12

Dear Bruce, Once again many thanks for helping.I am not using tracula. I used the dt_recon and I have done the registration for my FA data on the cvs space using the mri_cvs_register. I used the GLM group analysis method after I concatenate FA from individuals into one file and used mri_glmfit-sim \ --glmdir Group_Analysis.glmdir \ --grf 2 neg \ --cwpvalthresh .025 \ --overwrite to cache the significant clusters after multiple comparisons so I have the uncorrected and corrected significant map but I don't know how I can see if my FA is increasing or decreasing in controls group versus patients group. Please advise me. Thank you. Antonella ________________________________ From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> To: Antonella Kis <atorok9(a)yahoo.com> Sent: Wednesday, January 11, 2012 11:40 AM Subject: Re: [Freesurfer] Non_FA Group study Hi Antonella, can you post this type of question to the list so that others can answer? Do you mean a map across space or within each of the tracula fascicles? cheers Bruce On Wed, 11 Jan 2012, Antonella Kis wrote: > Dear Bruce, > > Many thanks for your reply and your help. > > I will be very grateful if you can give some advise on how I can do a > comparison between two groups for my FA data or in other words for FA group > analysis since from the significant map I can only find the p values how can > I see if there is an increase or decrease of the FA values for controls > versus patients? > > > Many thanks, > Antonella > > ____________________________________________________________________________ > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > To: Antonella Kis <atorok9(a)yahoo.com> > Cc: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu>; > "lzollei(a)nmr.mgh.harvard.edu" <lzollei(a)nmr.mgh.harvard.edu> > Sent: Wednesday, January 11, 2012 11:13 AM > Subject: Re: [Freesurfer] Non_FA Group study > > sure, that should be straightforward. > > cheers > Bruce > On Wed, 11 Jan 2012, Antonella Kis > wrote: > > > > > Dear FS team, > > > > > > Can use my results from the mri_cvs_register to do a non_FA group > analysis, > > more exactly I am interested on the mean diffusivity (adc.nii from > > dt_recon). > > > > > > Since from the significant map I can only find the p values how can I see > if > > there is an increase or decrease of the FA values or how can I do an FA > > comparison between two groups? > > > > Thank you very much for your time and help. > > Antonella > > > > > > > > > > > > > > > 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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watershed error in skull strip routine
by Holden, Timothy 11 Jan '12

11 Jan '12

Hi FS experts, I'm encountering an error in the Skull Strip routine with one brain that the FreeSurferWiki site and FS list don't seem to address. The error message is "mri_watershed Error: indices out of bounds" and results in an exit with errors (I've attached the recon-all.log). If I run "recon-all -skullstrip -wsthresh 35 -clean-bm -no-wsgcaatlas " or "recon-all -skullstrip -clean-bm -no-wsgcaatlas -gcut" on this brian the skull strip routine does finish but very little of the skull is removed and large chunks of the brain are removed in the brainmask file. I've checked the Talairach transform and it looks good but I did notice that the WM in the T1.mgz is not in the 110 range but more like 90. Do you think the problem is in the mri_normalize output and could be correct with control points? Your advice is greatly appreciated. Thanks, Tim Holden {Confidentiality Notice} The materials in this email are private and may contain Protected Healthcare Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return email. ***************************************************** Office Ph# (314) 362-7596 Program Office Ph# (314) 362-7245 Fax# (314) 362-7346 Timothy A. Holden, B.S.E. Research Scientist Cochlear Implant Program http://oto.wustl.edu/implant/ Washington University Medical School Department of Otolaryngology 660 S. Euclid Ave St. Louis, MO 63110-1007 **************************************************** The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return email.

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'fsaverage' directory
by swoodman＠nmr.mgh.harvard.edu 11 Jan '12

11 Jan '12

Hi all, We are trying to run exactly the same analysis, particularly the recon-all command, from two different directories. We've found that both directories have '/fsaverage' but that they are sourcing two different links/paths. Why is this and is there a difference in how analysis will be run/processed? The two directories in question are : /autofs/cluster/ablood/1/miriam/SD_recons AND /autofs/cluster/ablood/1/R01_Botox/R01BTX_recons We have been running everything in /R01BTX_recons, so we want this to be the model. I found out that: /autofs/cluster/ablood/1/miriam/SD_recons already has an fsaverage directory The difference between the fsaverage directories in /autofs/cluster/ablood/1/miriam/SD_recons AND /autofs/cluster/ablood/1/R01_Botox/R01BTX_recons Are the following: fsaverage in /autofs/cluster/ablood/1/miriam/SD_recons points to: fsaverage -> /usr/local/freesurfer/stable5_1_0/subjects/fsaverage and more specifically when I cd fsaverage from /autofs/cluster/ablood/1/miriam/SD_recons the pwd is: /autofs/cluster/freesurfer/centos4.0_x86_64/stable5_1_0/subjects/fsaverage Whereas: fsaverage in /autofs/cluster/ablood/1/R01_Botox/R01BTX_recons points to: fsaverage -> /usr/local/freesurfer/stable5/subjects/fsaverage and more specifically when I cd fsaverage from /autofs/cluster/ablood/1/R01_Botox/R01BTX_recons the pwd is: /autofs/cluster/freesurfer/centos4.0_x86_64/stable5/subjects/fsaverage Not sure if: 1. there is a significant difference between these fsaverages and if we need to be using exactly the same fsaverage in /autofs/cluster/ablood/1/miriam/SD_recons as in /autofs/cluster/ablood/1/R01_Botox/R01BTX_recons? Thank you! Sandra

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Building from source without GUIs
by Malcolm Tobias 11 Jan '12

11 Jan '12

I'm attempting to build the development branch of the source code. To reduce dependencies, I'm trying to build without any of the GUI support using the flags: --disable-all-apps --disable-gl-apps It's complaining about a missing dependency: configure: error: FATAL: libBLT not found. Check config.log. Set LDFLAGS or -- with-BLT-dir. but the instructions imply that BLT is only necessary for GUIs. Are there additional arguments that I need to pass to configure? Malcolm -- Malcolm Tobias 314.362.1594

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Re: [Freesurfer] Non_FA Group study
by Antonella Kis 11 Jan '12

11 Jan '12

Dear Bruce, Many thanks for your reply and your help. Can you please give me an advise on how I can do a comparison between two groups for my FA data or in other words for FA group analysis since from the significant map I can only find the p values how can I see if there is an increase or decrease of the FA values for controls versus patients? Many thanks, Antonella ________________________________ From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> To: Antonella Kis <atorok9(a)yahoo.com> Cc: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu>; "lzollei(a)nmr.mgh.harvard.edu" <lzollei(a)nmr.mgh.harvard.edu> Sent: Wednesday, January 11, 2012 11:13 AM Subject: Re: [Freesurfer] Non_FA Group study sure, that should be straightforward. cheers Bruce On Wed, 11 Jan 2012, Antonella Kis wrote: > > Dear FS team, > > > Can use my results from the mri_cvs_register to do a non_FA group analysis, > more exactly I am interested on the mean diffusivity (adc.nii from > dt_recon). > > > Since from the significant map I can only find the p values how can I see if > there is an increase or decrease of the FA values or how can I do an FA > comparison between two groups? > > Thank you very much for your time and help. > Antonella > > > > > > 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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Group Analysis for non-FA data
by Antonella Kis 11 Jan '12

11 Jan '12

Dear Lilla, I wonder if I can use my results from the mri_cvs_register to do a non_FA group study analysis, more exactly I am interested on the mean diffusivity (adc.nii from dt_recon). I hope I don't need to run again the registration again. Since from the significant map I can only find/ tells only about about the p values how can I see if there is an increase or decrease in FA values or how can I do an FA comparison between two groups? Thank you very much for your time and help. Antonella

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Re: [Freesurfer] GLM design question
by Douglas N Greve 11 Jan '12

11 Jan '12

Thanks to both Donald and Michael for catching my mistake about recommending sample-size weighting within the contrast (both responses are below). Depending upon the hypothesis being tested it is ok, but you're probably not going to be in a situation in which you will want to. doug -------------- from Donald McLaren ----------------------------------- Doug, From my understanding there are two questions that need to be asked before a decision is made: (1) Do I want the average across the groups OR Do I want the average of this cohort? The former should use equal weightings, while the latter should use the weighted average. Typically, people want the average of the groups, rather than the average of the cohort. The average of the cohort can be skewed toward the larger groups' means. An alternative would be to weight males and females based on the ratio of males and females that have the disease, in this way you are estimating the average of diseased individuals that is not prone to sampling bias. From the statistical perspective. The typical null hypothesis is that (males+females)/2=0. Thus, one should not weight the groups by the number of subjects. If the null hypothesis was healthy-diseased=0, then one would use the ratio of the diseased individuals in the population to avoid any bias in the sample. If the null hypothesis was healthy-diseased=0 in this sample, then one would use the ratio of the diseased individuals in this sample to avoid any bias in the sample. (2) Dealing with outliers. Small samples can easily have an outlier that would pull the mean away from its true value; however, the variance will be higher and less likely to produce a significant result. When you have very small samples, one might ask, is it worth including that group? In your case, if you only have 3 males, one might consider limiting the study to females. A final point, if there is a interaction effect, then they should never be averaged. Even if there is not an interaction, you can still gain power by splitting the groups because then you can model the variance of each group separately. Michael Harms wrote: > Hi Martijn, > Just to elaborate briefly on what Doug wrote, if you weight your > contrast vector by the sex ratio, you are however testing a very > different hypothesis. Specifically, whether a healthy population of 75% > female differs from a diseased population of 75% female. In that sense, > are you not really "controlling" for sex any more in the typical sense > of controlling for a non-balanced sample. (Rather, you are explicitly > hypothesizing a non-balanced sample). If you want to test the > hypothesis that the healthy and diseased subjects differ in a putative > balanced sample of 50% male/ 50% female, then you should *not* weight > your contrast vectors according to the sex ratio of your particular > sample. > > cheers, > -MH > > On Mon, 2012-01-09 at 18:13 -0500, Douglas N Greve wrote: > >> Hi Martijn, yes, that is a good thing to do! >> doug >> >> Martijn Steenwijk wrote: >> >>> Hi Doug, >>> >>> Thanks for your reply again. It's getting more and more clear now. >>> >>> I've however one question remaining, which is regarding the correction >>> for sex. What I did not tell (my fault ;-) ), is that 75% of the >>> cohort is female. Comparing the sex-corrected results with male-only >>> and female-only results, it appears to me that the relatively small >>> male-group partly 'drives' the results in the sex-corrected results. I >>> guess this is because the males and females are currently equally >>> weighted in the contrast matrices. Shouldn't the differences in sex >>> also be represented in the contrast matrices, like >>> [.25 .75 -.25 -.75 0 0 0 0 0 0 0 0] >>> [0 0 .25 .75 -.25 -.75 0 0 0 0 0 0] >>> [ .25 .75 0 0 -.25 -.75 0 0 0 0 0 0] >>> >>> ? Or am I wrong? >>> >>> Best, >>> Martijn >>> >>> >>> On Wed, Dec 21, 2011 at 5:45 PM, Douglas N Greve >>> <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: >>> >>> >>> Hi Martijn, sorry for the delay. Your contrast matrices look >>> correct. The differences between demeaning and not demeaning is >>> somewhat expected. When you do not demean, you are testing whether >>> there is a difference between groups at age=0 (ie, birth). When >>> you demean, you are testing for a difference at age=MeanAge. If >>> the slope of each group with respect to age is the same, then this >>> will yield the same result since the regression lines will be >>> parallel and the distance between parallel lines will always be >>> the same. If the slopes differ, then the distance will change with >>> age. For example, there will be an age where the lines cross. If >>> you test at this age, you are assured not to see a difference! For >>> this reason, it is better to test for a difference in the slopes, >>> and, if there is no difference, then reanalyze with DOSS which >>> forces the lines to be parallel. In your case, you found that >>> there is some difference in insula. If this is not the area that >>> you are interested in, then I would not worry about it. You should >>> just keep in mind that you should not try to draw conclusions from >>> this area. >>> doug >>> >>> Martijn Steenwijk wrote: >>> >>> Dear Doug, >>> >>> Thanks again for your reply. Based on that I did some further >>> work. >>> >>> I first demeaned the age of all subjects. Actually, I have a >>> third group which I would like to compare to, so my contrast >>> matrices will be [.5 .5 -.5 -.5 0 0 0 0 0 0 0 0] >>> [0 0 .5 .5 -.5 -.5 0 0 0 0 0 0] >>> [.5 .5 0 0 -.5 -.5 0 0 0 0 0 0] >>> to test for CT differences between all the groups while >>> correcting for age and sex. Surprisingly, I'm observing a big >>> difference in the results compared to the results without >>> demeaning. Could you explain the reson for this? In the >>> FSGD-examples (eg >>> http://surfer.nmr.mgh.harvard.edu/fswiki/FsgdFormat) age is >>> also not normalized. Does normalizing the variance to 1 also >>> influence the results? >>> Given this big difference, I started wondering whether it >>> would maybe be better to analyze the data in pairs of two >>> groups (and then demean by the mean of the two groups). Would >>> this be a better approach? >>> >>> Concerning your second suggestion: if I test the data for >>> differences in group slope, a number of small area's are >>> significantly different. Regions popping up are especially in >>> the neighborhood of the insula. Unfortunately this suggests >>> that I cannot use the DOSS model, or am I wrong? >>> >>> Looking forward to your reply, >>> With best regards, >>> Martijn >>> >>> >>> On Sat, Dec 10, 2011 at 7:16 PM, Douglas 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: >>> >>> Yes, that is correct, though I think your matrix should be >>> [.5 .5 >>> -.5 -.5 0 0 0 0]. You should also remove the mean from the age >>> (mean computed from all subjects). Or even better, first test >>> whether there is a group difference in age slope with [0 0 >>> 0 0 .5 >>> .5 -.5 -.5]. If there is nothing that is significant, then >>> re-run >>> your analysis using the Different Offset Same Slope (DOSS) >>> model >>> with this contrast [.5 .5 -.5 -.5 0]. >>> >>> doug >>> >>> >>> On 12/10/11 4:15 AM, Martijn Steenwijk wrote: >>> >>> >>> Dear all, >>> >>> >>> I’m relatively new with Freesurfer, but slowly getting >>> more and >>> more used to it’s great possibilities. To be ‘sure’, I’ve a >>> question about the design of a GLM. >>> >>> >>> I want to compare CT in Healthy Controls vs Diseased, >>> and control >>> for age and sex. It appears to me that factors (eg sex) >>> cannot be >>> used as covariate/variable, which forces me to model >>> them as a >>> separate class although I’m not interested in sex >>> differences. >>> This brings me to the following FSGD file: >>> >>> >>> # HcDis.fsgd >>> >>> GroupDescriptorFile 1 >>> >>> Title HcDis >>> >>> Class Hc_Male >>> >>> Class Hc_Female >>> >>> Class Dis_Male >>> >>> Class Dis_Female >>> >>> Variables Age >>> >>> Input subjid1 Hc_Male 35 >>> >>> Input subjid2 Dis_Female 30 >>> >>> …. >>> >>> >>> Then the difference between Hc and Dis, corrected for >>> age and sex >>> is given by the contrast matrix >>> >>> #Hc-vs-Dis.mtx >>> >>> 0.5 0.5 -0.5 -0.5 0 0 0 0 0 0 0 0 >>> >>> >>> Is this correct? >>> >>> >>> Best, >>> >>> Martijn >>> >>> >>> >>> >>> >>> _______________________________________________ >>> 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 >>> >>> >>> _______________________________________________ >>> 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 >>> >>> >>> 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 <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> >>> >>> >>> >> -- >> 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 >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

2 1

downsampling 4D volume
by ythomas 10 Jan '12

10 Jan '12

Hi, I am trying to downsample a 4D volume using mri_convert. However, it seems to be killing the 4 dimension. For example, if I do mri_convert -voxsize 4 4 4 tmp.mgz tmp444.mgz The original volume which is 256 x 256 x 256 x 120 becomes 64 x 64 x 64. Thanks, Thomas

4 7

Is building with OpenMP supported?
by Malcolm Tobias 10 Jan '12

10 Jan '12

After being able to build with GCC, I tried to add OpenMP support: [root@login002 freesurfer-dev-20120106]# ./configure --enable-openmp -disable- all-apps --with-mni-dir=/export/minc-1.4/ --with-vxl-dir=/export/vxl-1.13.0 --prefix=/scratch/mtobias/freesurfer-dev-gcc-openmp ... (Note: Mac OS X doesn't use crypt) checking for nccreate in -lnetcdf... no configure: error: FATAL: netcdf lib not found. Set LDFLAGS or --with-mni-dir. I don't believe there's a problem with the library: [root@login002 freesurfer-dev-20120106]# ls /export/minc-1.4/lib libEBTKS.a libminc.a libnetcdf.a libvolume_io.la perl5 libEBTKS.la libminc.la libvolume_io.a mni_autoreg [root@login002 freesurfer-dev-20120106]# nm /export/minc-1.4/lib/libnetcdf.a | grep nccreate 000000000000028d T nccreate and if I eliminate the "--enable-openmp" flag it configures fine. Depending on how well FreeSurfer is parallelized, OpenMP could be a great benefit for us here, but if it doesn't work too well, or isn't really supported, I can move on to try other things. Cheers, Malcolm -- Malcolm Tobias 314.362.1594

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