Freesurfer August 2013

freesurfer@nmr.mgh.harvard.edu

145 participants
268 discussions

Mapping data into segmented atlas
by Oscar Sotolongo Grau 05 Aug '13

05 Aug '13

Hi Freesurfers, I had run Freesurfer over a set of MRIs, extracted the volumes for different ROIs and correlated with another biomarkers using R. Now I want to represent the obtained correlations for the segmented ROIs into a brain template. Is there some automated way to do that with Freesurfer? or maybe with another tool? -- O. Sotolongo, <osotolongo(a)fundacioace.com> http://dfmf.uned.es/~osotolongo Tf. +34 652 575 178 Fundació ACE. Institut Català de Neurociències Aplicades. http://www.fundacioace.com

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Re: [Freesurfer] Segmentation Abnormalities Label
by Zhu, Alyssa 05 Aug '13

05 Aug '13

Hi, We were hoping to get these labels listed in FreeSurferColorLUT.txt. Does anyone know of any command lines that would get us this data? 100 Left-wm-intensity-abnormality 124 140 178 0 101 Left-caudate-intensity-abnormality 125 140 178 0 102 Left-putamen-intensity-abnormality 126 140 178 0 103 Left-accumbens-intensity-abnormality 127 140 178 0 104 Left-pallidum-intensity-abnormality 124 141 178 0 105 Left-amygdala-intensity-abnormality 124 142 178 0 106 Left-hippocampus-intensity-abnormality 124 143 178 0 107 Left-thalamus-intensity-abnormality 124 144 178 0 108 Left-VDC-intensity-abnormality 124 140 179 0 109 Right-wm-intensity-abnormality 124 140 178 0 110 Right-caudate-intensity-abnormality 125 140 178 0 111 Right-putamen-intensity-abnormality 126 140 178 0 112 Right-accumbens-intensity-abnormality 127 140 178 0 113 Right-pallidum-intensity-abnormality 124 141 178 0 114 Right-amygdala-intensity-abnormality 124 142 178 0 115 Right-hippocampus-intensity-abnormality 124 143 178 0 116 Right-thalamus-intensity-abnormality 124 144 178 0 117 Right-VDC-intensity-abnormality 124 140 179 0 Thanks, Alyssa ________________________________________ From: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] Sent: Monday, August 05, 2013 10:19 AM To: Zhu, Alyssa Subject: RE: [Freesurfer] Segmentation Abnormalities Label Hi Alyssa I don't think we label those explicitly. Presumably you could infer the structure from surrounding labels though (or from spatial priors I guess) Bruce On Mon, 5 Aug 2013, Zhu, Alyssa wrote: > Hi Bruce, > > Thanks for the reply. > > Sorry if I worded my e-mail badly, but I was actually wondering if there was a way to obtain those labels as we haven't seen them in our stats files. We did get some voxels labeled as non-WM hypointensities, but they are in various parts of the basal ganglia and would have to be manually differentiated (e.g. caudate vs. putamen). Is there some way they could be automatically parcellated into the intensity abnormality labels listed in the FreeSurferColorLUT.txt file. In other words, is there a way we can opt for those parcellations/labels in the recon-all or aparcstats2table commands? > > Thanks again, > Alyssa > > ________________________________________ > From: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] > Sent: Friday, August 02, 2013 7:35 PM > To: Zhu, Alyssa > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Segmentation Abnormalities Label > > Hi Alyssa, > > the orbital stuff might be fat that has shifted into brain, for which > there's really nothing that can be done except fix the acquisition > (change the read-out direction or increase the bandwidth or both). Not sure > what's up with the other spot. Is the nearby white matter intensity > significantly less than 110? If so, some control points in the wm might > help. If not you would need to upload the dataset so we can take a look > Bruce > > > On Sat, 3 > Aug 2013, Zhu, Alyssa wrote: > >> Hi, >> >> Is there a way to get the various intensity abnormality labels (100-117) >> seen in the FreeSurferColorLUT.txt file (e.g. via a different command line >> option)? Thus far we've only been getting the WM-hypointensities (77) and >> non-WM-hypointensities (80) labels. I read in another thread that some >> labels are no longer used in current versions (my lab is using v5.1). Is >> that the case here? >> >> Thanks, >> Alyssa >> >> >> > > > 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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Monte Carlo
by Peter Boulos 05 Aug '13

05 Aug '13

Good afternoon, I am getting much different results in my QDEC before and after running monte carlo cluster correction. Upon initially running the QDEC I have what appears to be a significant group difference in the prefrontal region that does not show up after I run the Monte Carlo but at the same time there appears to be no result in the postcentral gyrus region prior to running the Monte Carlo but after running it, there is a huge result in that region. Is there something I missed? Peter

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Error with recon-all: You are trying to re-run an existing subject
by Joseph Andreano 05 Aug '13

05 Aug '13

Hi All, I'm trying to use recon-all on some structural data, and when I drop the command (specifically, recon-all -i /cluster/iaslab/SPAR/mri/recon/3danat/003/001.mgz -subjid SPAR_016_130708), I get this error message: ERROR: You are trying to re-run an existing subject with (possibly) new input data (-i). If this is truly new input data, you should delete the subject folder and re-run, or specify a different subject name. If you are continuing an analysis of an existing subject, then omit all -i flags. I have tried all the options suggested in the error message, and none work. I can't delete the subject folder, because no such folder exists. I tried running the command with a different subject name, and although the command appeared to complete without error, no folder with the new name was created, and no files were generated. I tried removing the -i flags, and I got this: ERROR: nothing to do. Any suggestions? Thanks, Joe Andreano _________________________________ Joseph M. Andreano, PhD Postdoctoral Researcher Interdisciplinary Affective Science Laboratory Massachusetts General Hospital _________________________________

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Re: [Freesurfer] Fwd: infant atlas segmentation
by Mark Plantz 05 Aug '13

05 Aug '13

Just as an update, it turns out that my segmentation volume had been slightly altered during the conversion from .nii to .mgz. I completely forgot to use the -rt nearest flag to prevent the labels from becoming distorted. That is why the segmentation looked so fuzzy with various regions labeled incorrectly. Apparently, I should check the basics before overcomplicating the problem, haha. Thanks for the help everyone! On Thu, Aug 1, 2013 at 9:36 AM, Mark Plantz < markplantz2016(a)u.northwestern.edu> wrote: > Sounds good. I also just realized that the segmentation values are varying > from 0-255, which makes me think that the file is only designed for the > grayscale/heat/etc. settings [where 0 is darkest regions and 255 is > brightest regions]. Is that a valid assumption? Also, if this is the case, > would it be impossible to create a .gca file using mri_ca_train with these > files? > > Thanks for the help. > > MP > > > On Wed, Jul 31, 2013 at 8:43 PM, Douglas Greve <greve(a)nmr.mgh.harvard.edu>wrote: > >> >> Just make sure that you create a new file and do not repeat index numbers. >> >> >> On 7/31/13 2:02 PM, Mark Plantz wrote: >> >> That makes sense. Wouldn't that cause there to be some overlap between >> different regions, since the same index #'s used by the two programs >> (FreeSurfer & MRIcro) correspond to different brain regions? >> >> >> On Tue, Jul 30, 2013 at 12:50 PM, Douglas Greve < >> greve(a)nmr.mgh.harvard.edu> wrote: >> >>> >>> for every line in that file, you will need to create a line in the new >>> LUT, something like >>> >>> >>> 8 Frontal_Mid_R 0 255 0 0 >>> >>> This will make the right mid frontal green = (0,255,0) >>> >>> >>> >>> >>> On 7/30/13 9:55 AM, Mark Plantz wrote: >>> >>> Hmm, so I received the text part of the LUT. Looks like this is >>> completely different from the segmented regions that we would want. >>> [attached]. Can't seem to understand how this text file could be related to >>> the default FreeSurfer LUT. It looks like the labeling for an AAL map. This >>> probably wont' work will it? >>> >>> - Mark >>> >>> >>> On Tue, Jul 30, 2013 at 8:47 AM, Bruce Fischl < >>> fischl(a)nmr.mgh.harvard.edu> wrote: >>> >>>> the UNC one? No, you should ask them >>>> On Tue, 30 Jul 2013, Mark Plantz wrote: >>>> >>>> >>>>> >>>>> ---------- Forwarded message ---------- >>>>> From: Mark Plantz <markplantz2016(a)u.northwestern.edu> >>>>> Date: Tue, Jul 30, 2013 at 8:39 AM >>>>> Subject: Re: [Freesurfer] infant atlas segmentation >>>>> To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >>>>> >>>>> >>>>> Just opened up the default FreeSurferColorLUT.txt file. So it looks >>>>> like all >>>>> I have to change is the #No. column of the file, to match the ones in >>>>> the >>>>> other LUT used. >>>>> I actually just received the MRIcro .lut file from the UNC group. >>>>> [attached] >>>>> >>>>> Hopefully this will help with the conversion. However, I still have to >>>>> figure out how to open the file. Any ideas? >>>>> >>>>> >>>>> >>>>> >>>>> On Tue, Jul 30, 2013 at 8:25 AM, Bruce Fischl < >>>>> fischl(a)nmr.mgh.harvard.edu> >>>>> wrote: >>>>> Hi Mark >>>>> >>>>> creating a FreeSurfer LUT really isn't that hard. Have you >>>>> looked at our standard one? Probably we have the names you >>>>> already want and you just need to change our indices to match >>>>> the ones in your segmentation file (and save it as a different >>>>> LUT) >>>>> >>>>> cheers >>>>> Bruce >>>>> >>>>> On Tue, 30 Jul 2013, Mark Plantz wrote: >>>>> >>>>> Turns out that the files had been labeled using a >>>>> color LUT in a program >>>>> called MRIcro. I am now installing this program >>>>> simply to access the LUT. >>>>> Will it be as simple as exchanging the index values >>>>> from this LUT to a >>>>> custom LUT in FreeSurfer? >>>>> >>>>> >>>>> On Tue, Jul 30, 2013 at 12:35 AM, Douglas Greve >>>>> <greve(a)nmr.mgh.harvard.edu> >>>>> wrote: >>>>> >>>>> The problem is that you need to create a >>>>> completely new LUT. The >>>>> labels that get displayed with the standard >>>>> LUT are going to be >>>>> totally random with respect to what they >>>>> should display. >>>>> >>>>> On 7/29/13 2:20 PM, Mark Plantz wrote: >>>>> Hi Doug, >>>>> Thanks for the reply. I will definitely go into >>>>> the LUT and >>>>> change those values to some specific region. My main >>>>> concern is >>>>> that I think all of these "out of bounds" labels are >>>>> the >>>>> symptoms of some larger problem. The segmentation >>>>> looks very >>>>> strange as compared to a typical segmentation (i.e. >>>>> an >>>>> 'aseg.mgz' file). In fact, the segmentation appears >>>>> to be >>>>> labeling "left-<region" in the right hemisphere. >>>>> Have you seen a >>>>> segmentation file that looks like the once I >>>>> attached before? I >>>>> am used to seeing segmentation files such as the one >>>>> attached to >>>>> this e-mail. >>>>> >>>>> - Mark >>>>> >>>>> >>>>> On Mon, Jul 29, 2013 at 12:28 PM, Douglas Greve >>>>> <greve(a)nmr.mgh.harvard.edu> wrote: >>>>> >>>>> Mark, the only thing that is wrong with the >>>>> out of >>>>> bounds regions is that they are not >>>>> represented in >>>>> the LUT. Once you add an index corresponding >>>>> to the >>>>> index of the segmentation to the LUT, it will >>>>> not >>>>> show up as "out of bounds". The brain mask has >>>>> nothing to do with it. >>>>> best >>>>> doug >>>>> >>>>> >>>>> >>>>> On 7/29/13 12:50 PM, Mark Plantz wrote: >>>>> Sorry about that. I received the manual >>>>> segmentations from a UNC medicalgroup< >>>>> http://www.med.unc.edu/bric/ideagroup/free-softwares/unc-infant-0-1-2 >>>>> -atla >>>>> ses>. I actually asked the main researcher >>>>> about the out of bounds regions. He thinks >>>>> that as long as the segmented file lines up >>>>> with the input volumes, a few out of bounds >>>>> regions might be OK. However, these seg >>>>> volumes look very different from a typical >>>>> .aseg volume that I am used to seeing after >>>>> recon-all is run. >>>>> Maybe the segmentation is simply incompatible with >>>>> FreeSurfer? >>>>> >>>>> Thanks for the help. These files are a nightmare! >>>>> >>>>> - MP >>>>> >>>>> >>>>> On Mon, Jul 29, 2013 at 11:40 AM, Bruce Fischl >>>>> <fischl(a)nmr.mgh.harvard.edu> wrote: >>>>> can you cc the list please? Maybe we >>>>> should start over. Where did you get the >>>>> manual segmentations from? >>>>> >>>>> On Mon, 29 Jul 2013, Mark Plantz wrote: >>>>> >>>>> Ahh, right. So it looks like >>>>> the red regions appear to be >>>>> averaged around 248. I am >>>>> not sure why that is the >>>>> case or if it has >>>>> any significance. I attached >>>>> a screen shot for >>>>> reference. >>>>> >>>>> >>>>> On Mon, Jul 29, 2013 at >>>>> 11:29 AM, Bruce Fischl >>>>> <fischl(a)nmr.mgh.harvard.edu> >>>>> wrote: >>>>> it isn't a >>>>> registration file. You >>>>> should just specify it as a >>>>> volume on the freeview >>>>> command line, the same as >>>>> brainmask.mgz >>>>> >>>>> On Mon, 29 Jul 2013, >>>>> Mark Plantz wrote: >>>>> >>>>> I actually tried >>>>> to view the brainmask.mgz >>>>> file with the segmentation >>>>> file [Freeview calls it >>>>> 'registration >>>>> file' I believe]. >>>>> For some reason, >>>>> the file will load without >>>>> segmentation, but when I >>>>> attempt to add the >>>>> registration >>>>> file, I get an >>>>> error >>>>> message: >>>>> "Failed to load >>>>> MRI >>>>> ~/.../../../brainmask.mgz >>>>> >>>>> Could this >>>>> potentially be part of the >>>>> problem? >>>>> >>>>> Thanks >>>>> >>>>> MP >>>>> >>>>> >>>>> On Mon, Jul 29, >>>>> 2013 at 10:57 AM, Mark >>>>> Plantz >>>>> <markplantz2016(a)u.northwestern.edu> >>>>> wrote: >>>>> >>>>> It looks >>>>> like the values vary from >>>>> 20-120 depending on which >>>>> region I run the cursor >>>>> over. >>>>> However, aren't >>>>> those the >>>>> values >>>>> that correspond to the >>>>> brain.mgz regions? Is there >>>>> another way to find the >>>>> segmentation >>>>> values? >>>>> >>>>> >>>>> On Mon, Jul 29, >>>>> 2013 at 10:37 AM, Bruce >>>>> Fischl >>>>> <fischl(a)nmr.mgh.harvard.edu> >>>>> wrote: >>>>> I mean the >>>>> segmentation values that >>>>> give you the "out of bounds" >>>>> message >>>>> On Mon, 29 >>>>> Jul 2013, Mark Plantz wrote: >>>>> >>>>> Hi >>>>> Bruce, >>>>> Do >>>>> you mean the brainmask.mgz >>>>> values? I'm not sure what >>>>> the segmentation #'s exactly >>>>> are. >>>>> >>>>> >>>>> Thanks! >>>>> >>>>> MP >>>>> >>>>> >>>>> On >>>>> Mon, Jul 29, 2013 at 10:17 >>>>> AM, Bruce Fischl >>>>> <fischl(a)nmr.mgh.harvard.edu> >>>>> wrote: >>>>> >>>>> Hi Mark >>>>> >>>>> >>>>> >>>>> what #s are those >>>>> segmentations? It should be >>>>> trivial to just add them to >>>>> the end of >>>>> the >>>>> LUT. >>>>> I wouldn't let them be >>>>> >>>>> out of bounds as there >>>>> might be code around that >>>>> might ignore them then. >>>>> >>>>> >>>>> cheers >>>>> >>>>> Bruce >>>>> >>>>> >>>>> On Mon, 29 Jul 2013, Mark >>>>> Plantz wrote: >>>>> >>>>> >>>>> Hi Doug, >>>>> >>>>> Thanks for >>>>> the reply. After doing some >>>>> research, it looks like >>>>> messing >>>>> with the >>>>> LUT >>>>> might be a >>>>> >>>>> risky decision [and >>>>> way >>>>> >>>>> out of my >>>>> abilities!]. >>>>> >>>>> >>>>> If I were to use >>>>> this segmentation file to >>>>> create a .gca atlas using >>>>> the >>>>> command >>>>> >>>>> mri_ca_train, do you >>>>> >>>>> think it would yield >>>>> >>>>> problems or be >>>>> inaccurate? I guess what I >>>>> am trying to figure out is >>>>> if the >>>>> color >>>>> >>>>> lookup values are even >>>>> >>>>> significant when >>>>> using >>>>> >>>>> the segmentation >>>>> file to create an atlas? >>>>> >>>>> >>>>> Thanks for all of >>>>> the help with this. >>>>> >>>>> >>>>> Best, >>>>> >>>>> >>>>> MP >>>>> >>>>> >>>>> p.s. I attached the >>>>> photo of the segmentation >>>>> volume because this e-mail >>>>> is sort >>>>> of >>>>> old >>>>> >>>>> >>>>> >>>>> On Wed, Jul 24, 2013 >>>>> at 2:39 PM, Douglas N Greve >>>>> <greve(a)nmr.mgh.harvard.edu> >>>>> wrote: >>>>> >>>>> you need a new >>>>> LUT. See my comment from a >>>>> few emails ago. >>>>> >>>>> On 07/24/2013 >>>>> 03:29 PM, Mark Plantz wrote: >>>>> >>>>> I'm not >>>>> actually quite sure what it >>>>> means either. When I use the >>>>> command >>>>> line: >>>>> >>>>> >>>>> tkmedit >>>>> $Subject brain.mgz >>>>> -segmentation <seg.mgz>, >>>>> >>>>> >>>>> I can run the >>>>> cursor over various regions >>>>> and the name of the region >>>>> should pop >>>>> up. >>>>> For some >>>>> >>>>> reason, the red >>>>> >>>>> regions are >>>>> simply labeled as "out of >>>>> bounds." >>>>> >>>>> >>>>> I'll keep >>>>> messing with tkmedit and let >>>>> you know if I find out what >>>>> the >>>>> problem >>>>> is. >>>>> >>>>> >>>>> Thanks guys! >>>>> >>>>> >>>>> MP >>>>> >>>>> >>>>> >>>>> On Wed, Jul 24, 2013 >>>>> at 2:26 PM, Douglas N Greve >>>>> <greve(a)nmr.mgh.harvard.edu >>>>> >>>>> >>>>> <mailto:greve@nmr.mgh.harvard.edu>> >>>>> >>>>> wrote: >>>>> >>>>> >>>>> what do you mean >>>>> that they are out of bounds? >>>>> >>>>> >>>>> On 07/24/2013 >>>>> 03:25 PM, Mark Plantz wrote: >>>>> >>>>> >>>>> I guess the >>>>> problem is that those >>>>> regions should not be out of >>>>> >>>>> bounds. >>>>> Maybe I need to create a new >>>>> Lookup Table for the >>>>> >>>>> infant >>>>> mri's? Is that possible to >>>>> do? >>>>> >>>>> >>>>> >>>>> On Wed, Jul >>>>> 24, 2013 at 2:21 PM, Douglas >>>>> N Greve >>>>> >>>>> >>>>> <greve(a)nmr.mgh.harvard.edu >>>>> <mailto:greve@nmr.mgh.harvard.edu> >>>>> >>>>> >>>>> <mailto:greve@nmr.mgh.harvard.edu >>>>> >>>>> >>>>> <mailto:greve@nmr.mgh.harvard.edu>>> >>>>> wrote: >>>>> >>>>> >>>>> Hi Mark, >>>>> please post to the list and >>>>> not to me. >>>>> >>>>> thanks >>>>> >>>>> doug >>>>> >>>>> >>>>> On >>>>> 07/24/2013 03:21 PM, Mark >>>>> Plantz wrote: >>>>> >>>>> >>>>> I >>>>> guess the problem is that >>>>> those regions should not >>>>> >>>>> be out of >>>>> >>>>> >>>>> bounds. Maybe I need to >>>>> create a new Lookup Table >>>>> for the >>>>> >>>>> >>>>> infant mri's? Is that >>>>> possible to do? >>>>> >>>>> >>>>> >>>>> On >>>>> Wed, Jul 24, 2013 at 2:15 >>>>> PM, Douglas N Greve >>>>> >>>>> >>>>> <greve(a)nmr.mgh.harvard.edu >>>>> >>>>> >>>>> <mailto:greve@nmr.mgh.harvard.edu> >>>>> >>>>> >>>>> <mailto:greve@nmr.mgh.harvard.edu >>>>> >>>>> >>>>> <mailto:greve@nmr.mgh.harvard.edu>> >>>>> >>>>> >>>>> <mailto:greve@nmr.mgh.harvard.edu >>>>> >>>>> >>>>> <mailto:greve@nmr.mgh.harvard.edu> >>>>> >>>>> >>>>> <mailto:greve@nmr.mgh.harvard.edu >>>>> >>>>> >>>>> <mailto:greve@nmr.mgh.harvard.edu>>>> >>>>> wrote: >>>>> >>>>> >>>>> >>>>> >>>>> what is the problem exactly? >>>>> The fact that there >>>>> >>>>> are red >>>>> >>>>> >>>>> regions >>>>> >>>>> >>>>> or that that the red regions >>>>> are labeled as "Out of >>>>> >>>>> >>>>> Bounds"? If >>>>> >>>>> >>>>> the latter, you will need to >>>>> create a LUT that >>>>> >>>>> matches your >>>>> >>>>> >>>>> regions. the out of bounds >>>>> means that the index in the >>>>> >>>>> >>>>> volume does >>>>> >>>>> >>>>> not match an index in the >>>>> LUT. >>>>> >>>>> >>>>> doug >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> On 07/24/2013 01:26 PM, Mark >>>>> Plantz wrote: >>>>> >>>>> >>>>> >>>>> Finally got the >>>>> registration to work. >>>>> However, it >>>>> >>>>> >>>>> looks like >>>>> >>>>> >>>>> the out of bounds >>>>> regions (in red) are still >>>>> >>>>> present >>>>> (even >>>>> >>>>> >>>>> though the regions are >>>>> well within our >>>>> >>>>> boundaries). >>>>> Is >>>>> >>>>> that >>>>> >>>>> >>>>> expected since they were >>>>> labeled in the original >>>>> >>>>> >>>>> segmentation >>>>> >>>>> >>>>> volume? Is there anyway >>>>> to correct those? >>>>> >>>>> >>>>> >>>>> Thanks for all of the >>>>> help! >>>>> >>>>> >>>>> >>>>> - Mark >>>>> >>>>> >>>>> p.s. I attached a >>>>> picture of the original >>>>> >>>>> brain.mgz >>>>> file >>>>> >>>>> >>>>> viewed with the >>>>> corrected segmentation >>>>> volume >>>>> >>>>> >>>>> >>>>> >>>>> On Wed, Jul 24, 2013 at >>>>> 12:22 PM, Mark Plantz >>>>> >>>>> >>>>> >>>>> <markplantz2016(a)u.northwestern.edu >>>>> >>>>> >>>>> >>>>> <mailto:markplantz2016@u.northwestern.edu> >>>>> >>>>> >>>>> >>>>> <mailto:markplantz2016@u.northwestern.edu >>>>> >>>>> >>>>> >>>>> <mailto:markplantz2016@u.northwestern.edu>> >>>>> >>>>> >>>>> >>>>> >>>>> <mailto:markplantz2016@u.northwestern.edu >>>>> >>>>> >>>>> >>>>> <mailto:markplantz2016@u.northwestern.edu> >>>>> >>>>> >>>>> >>>>> <mailto:markplantz2016@u.northwestern.edu >>>>> >>>>> >>>>> >>>>> <mailto:markplantz2016@u.northwestern.edu>>> >>>>> >>>>> >>>>> >>>>> >>>>> <mailto:markplantz2016@u.northwestern.edu >>>>> >>>>> >>>>> >>>>> <mailto:markplantz2016@u.northwestern.edu> >>>>> >>>>> >>>>> >>>>> <mailto:markplantz2016@u.northwestern.edu >>>>> >>>>> >>>>> >>>>> <mailto:markplantz2016@u.northwestern.edu>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> <mailto:markplantz2016@u.northwestern.edu >>>>> >>>>> >>>>> >>>>> <mailto:markplantz2016@u.northwestern.edu> >>>>> >>>>> >>>>> >>>>> <mailto:markplantz2016@u.northwestern.edu >>>>> >>>>> >>>>> >>>>> <mailto:markplantz2016@u.northwestern.edu>>>>> >>>>> wrote: >>>>> >>>>> >>>>> >>>>> Finally got the >>>>> registration to work. >>>>> >>>>> However, it >>>>> >>>>> >>>>> looks >>>>> >>>>> >>>>> like the >>>>> >>>>> >>>>> out of bound regions >>>>> (in red) are still >>>>> >>>>> prevalent. >>>>> >>>>> >>>>> Is >>>>> that >>>>> >>>>> >>>>> expected since they >>>>> were present in the >>>>> >>>>> original >>>>> >>>>> >>>>> segmentation >>>>> >>>>> >>>>> volume? Would there >>>>> >>>>> be anyway to correct >>>>> >>>>> those? >>>>> >>>>> >>>>> >>>>> Thanks for all the >>>>> help! >>>>> >>>>> >>>>> >>>>> - MP >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> On Wed, Jul 24, 2013 >>>>> at 11:11 AM, Mark Plantz >>>>> >>>>> >>>>> >>>>> >>>>> <markplantz2016(a)u.northwestern.edu >>>>> >>>>> >>>>> >>>>> <mailto:markplantz2016@u.northwestern.edu> >>>>> >>>>> >>>>> >>>>> <mailto:markplantz2016@u.northwestern.edu >>>>> >>>>> >>>>> >>>>> <mailto:markplantz2016@u.northwestern.edu>> >>>>> >>>>> >>>>> >>>>> >>>>> <mailto:markplantz2016@u.northwestern.edu >>>>> >>>>> >>>>> >>>>> <mailto:markplantz2016@u.northwestern.edu> >>>>> >>>>> >>>>> >>>>> <mailto:markplantz2016@u.northwestern.edu >>>>> >>>>> >>>>> >>>>> <mailto:markplantz2016@u.northwestern.edu>>> >>>>> >>>>> >>>>> >>>>> >>>>> <mailto:markplantz2016@u.northwestern.edu >>>>> >>>>> >>>>> >>>>> <mailto:markplantz2016@u.northwestern.edu> >>>>> >>>>> >>>>> >>>>> <mailto:markplantz2016@u.northwestern.edu >>>>> >>>>> >>>>> >>>>> <mailto:markplantz2016@u.northwestern.edu>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> <mailto:markplantz2016@u.northwestern.edu >>>>> >>>>> >>>>> >>>>> <mailto:markplantz2016@u.northwestern.edu> >>>>> >>>>> >>>>> >>>>> <mailto:markplantz2016@u.northwestern.edu >>>>> >>>>> >>>>> >>>>> <mailto:markplantz2016@u.northwestern.edu>>>>> >>>>> wrote: >>>>> >>>>> >>>>> >>>>> Nevermind, it >>>>> turned out to be a >>>>> >>>>> permissions >>>>> >>>>> >>>>> issue. >>>>> >>>>> >>>>> Thanks! >>>>> >>>>> >>>>> >>>>> >>>>> On Wed, Jul 24, >>>>> 2013 at 10:12 AM, Mark >>>>> >>>>> >>>>> Plantz >>>>> >>>>> >>>>> >>>>> <markplantz2016(a)u.northwestern.edu >>>>> >>>>> >>>>> >>>>> <mailto:markplantz2016@u.northwestern.edu> >>>>> >>>>> >>>>> >>>>> <mailto:markplantz2016@u.northwestern.edu >>>>> >>>>> >>>>> >>>>> <mailto:markplantz2016@u.northwestern.edu>> >>>>> >>>>> >>>>> >>>>> >>>>> <mailto:markplantz2016@u.northwestern.edu >>>>> >>>>> >>>>> >>>>> <mailto:markplantz2016@u.northwestern.edu> >>>>> >>>>> >>>>> >>>>> <mailto:markplantz2016@u.northwestern.edu >>>>> >>>>> >>>>> >>>>> <mailto:markplantz2016@u.northwestern.edu>>> >>>>> >>>>> >>>>> >>>>> >>>>> <mailto:markplantz2016@u.northwestern.edu >>>>> >>>>> >>>>> >>>>> <mailto:markplantz2016@u.northwestern.edu> >>>>> >>>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)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. >>> >>> >> >> >

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Controlling for shape (and size) of a ROI in co-registration
by pfotiad＠nmr.mgh.harvard.edu 05 Aug '13

05 Aug '13

Hi FS Community, Is there a way to control for the size and shape of a ROI when applying co-registration? For instance, I drew a ROI in a scan through freesurfer, and then when I coregistered that ROI to another scan, the resulting ROI had a different shape and number of voxels compared to the original ROI. IS there a way to control for that? Thank you for your time. Best, Panos

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trouble with bias correction
by Keith Jamison 05 Aug '13

05 Aug '13

Some of the T1 scans I'm working with have pretty severe intensity inhomogeneity, with the signal dropping off significantly toward the sides of the head. This is not being adequately corrected and the segmentation is missing considerable portions of gray matter in those areas. I've played with some bias correction techniques but so far I have not been very successful. In the attached screenshots, you can see the problem on the left side of the brain. The skull drops down significantly and in the ribbon file we lose all of the gray matter in that area. Is there a way to use control points to specify gray matter as well as white? Is there another obvious fix for this kind of problem? Thanks! -Keith

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long_mris_slopes sign of do-rate
by vbrunsch＠nmr.mgh.harvard.edu 05 Aug '13

05 Aug '13

Dear Freesurfer experts, I have followed the LongitudinalTutorial with two time points + two groups and now, after looking at the output of the qdec analysis, I just want to make sure I haven't made a sign error as for the control group the difference is as expected around 0 but for the experimental group I see negative values (= thinning?) all over the place which seems weird, just want to make sure I got this right: I set the time variable to 0 for the baseline scan and to 1 for the after-intervention-scan. Is it correct that for do-rate the calculation is then only <thickness of tp2> - <thickness of tp1> and not the other way around? I ask because in the long_mris_slopes -help it says that do-rate would yield the "thinning in mm/time" and if this means that a positive value stands for thinning then this would contradict what I understood from the Tutorial where it says for the rate "thick2-thick1" is calculated, so a positive value should mean "thickening". Also, how does long_mris_slopes know which one is tp1 and which one is tp2? I assume it takes the first entry in the fsid column of long.qdec.table.dat as tp1 and the second entry below as tp2? Hm, I see no other possibilities of making a sign error during the whole process, did anyone report a similar issue? Thanks for your help! Best, Vincent

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Re: [Freesurfer] TR,TE,TI,FA variability w/ mri_ca_train
by Mark Plantz 05 Aug '13

05 Aug '13

For some reason, when I run that command, I get the following output: Input volume is : seg_mov Output volume is : seg_mov_2 There are no errors, but when I check "mri_info" of the output file, the TR, TE, etc. values are still non-zero. Any ideas what could cause that to happen? Thanks! MP On Mon, Aug 5, 2013 at 11:35 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > yes, I think so > > On Mon, 5 Aug 2013, Mark Plantz wrote: > > thank you. Would the command simply be something like this: mri_modify >> -tr 0 -te 0 -ti 0 -fa 0 <input.mgz> <output.mgz> ? >> >> >> On Thu, Aug 1, 2013 at 1:41 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> wrote: >> Hi Mark >> >> the formatting got messed up so I can't parse your table. You can >> get around this using mri_modify, and just setting >> everything to 0. As for the effects, look at the images and see >> what you think. >> >> cheers >> Bruce >> >> On Thu, 1 Aug 2013, Mark Plantz wrote: >> >> Hello freesurfers, >> I currently have a series of images with various >> TR,TE,TI,FA values. I >> would like to use mri_ca_train to create a .gca atlas based >> on these >> segmented volumes. Unfortunately, they all have slightly >> different control >> parameters (TR,TE,TI,FA). Is there any way around this >> problem, or would it >> be best to break the subjects into multiple groups with the >> same control >> parameters? >> >> Here are the various parameters: [each row is a subject] >> >> TR >> TE >> TI >> flip angle >> 9.38 >> 3.86 >> 450 >> 12 >> 9.34 >> 3.86 >> 450 >> 12 >> 9.38 >> 3.86 >> 450 >> 12 >> 9.38 >> 3.86 >> 450 >> 12 >> 9.34 >> 3.86 >> 450 >> 12 >> 9.44 >> 3.87 >> 450 >> 12 >> 9.39 >> 3.86 >> 450 >> 12 >> 2065.98 >> 7.61 >> 886.92 >> 90 >> 9.45 >> 3.89 >> 450 >> 12 >> 9.41 >> 3.87 >> 450 >> 12 >> 9.41 >> 3.87 >> 450 >> 12 >> 9.42 >> 3.91 >> 450 >> 12 >> 9.38 >> 3.86 >> 450 >> 12 >> 9.38 >> 3.86 >> 450 >> 12 >> 9.44 >> 3.86 >> 450 >> 12 >> 9.44 >> 3.86 >> 450 >> 12 >> 9.38 >> 3.86 >> 450 >> 12 >> 9.38 >> 3.86 >> 450 >> 12 >> 9.38 >> 3.86 >> 450 >> 12 >> 9.34 >> 3.86 >> 450 >> 12 >> 9.34 >> 3.86 >> 450 >> 12 >> 9.39 >> 3.86 >> 450 >> 12 >> 1900 >> 2.6 >> 900 >> 9 >> 1900 >> 2.6 >> 900 >> 9 >> 1900 >> 2.6 >> 900 >> 9 >> 9.41 >> 3.87 >> 450 >> 12 >> 9.41 >> 3.87 >> 450 >> 12 >> 9.41 >> 3.87 >> 450 >> 12 >> 1900 >> 2.6 >> 900 >> 9 >> 9.41 >> 3.87 >> 450 >> 12 >> 1900 >> 2.6 >> 900 >> 9 >> 1900 >> 2.6 >> 900 >> 9 >> >> Thank you in advance. >> >> -Mark >> >> >> >> >> >> 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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hemispheric masks?
by John Richey 05 Aug '13

05 Aug '13

Dear freesurfer experts, I was wondering whether there is an existing mask for the left and right hemispheres for fsaverage. I can't seem to find any documentation of this, but perhaps I am missing something? Thanks in advance, John.

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Freesurfer August 2013