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30090 discussions

mri_ms_fitparms_questions
by dgw 25 Apr '13

25 Apr '13

I have run mri_ms_fitparms (version 5.1.0) on phantom data from two multiecho flash volumes (5 and 20 degrees with 8 echos: 1.67ms - 14.83ms in 1.88ms steps) at 7T utilizing a b1 map for correction. How does mri_ms_fitparms know the field strength (I can't figure out where the information is when I read the mgz files using MRIread.m)? I notice that the T1 volume seems to have graded steps of 5ms. Is this due to the table of 1ms stepped T1 values in the table described in Fischl et al. 2004 (and the data in this case being collected at 7T)? Is there any way to increase the sensitivity? Interestingly, this effect seems to only have a small effect on the values of the PD.mgz; however, from the 2004 Fischl paper, I would have expected it to have a large effect. What concerns should I have about using the PD.mgz to represent the Equilibrium Magnetization in terms of accuracy of the values? Thank You, Dan

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Correcting bad segmentation/WM surfacing
by Jonathan Holt 25 Apr '13

25 Apr '13

See attached image for reference. Large area has been incorrectly segmented as WM, also WM surface has completely been skipped over. Planning to remove segmentation in that area and run recon-all again, is this correct or should something else be done to alleviate issue. Worth noting this issue is only in one hemisphere.

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convert labels to volumetric masks
by limengsecret 25 Apr '13

25 Apr '13

Dear FreeSurfers, I want to convert cortical labels to volumetric masks, and I run the following commands: 1. tkregister2 �Cmov sub/mri/rawavg.mgz �Cnoedit �Cs sub �Cregheader �Creg ./register.dat 2. mri_label2vol �Clabel ./lh.entorhinal.label �Ctemp sub/mri/rawavg.mgz �Csubject sub �Chemi lh �Co sub_lh_entorhinal.nii.gz �Cproj frac 0 1 .1 �Cfillthresh .3 �Creg ../mri/register.dat if I do not run the recon-all command, could I change the rawavg.mgz to sub.nii (original data)? The second problem is that when I convert the annotation file to volumetric mask, whether I should convert the file to labels using mri_annotation2label first, then run the commands as decribed above, or there is a way that could convert the annotation file to volumetric mask directly? The last problem is that how to convert the .curv file and .w file to volumetic mask? Any help will be very appreciated. Best wishes, Meng

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System recommendations for Freesurfer
by Graham Wideman 25 Apr '13

25 Apr '13

Hi all, I am looking for current recommendations for specs for a desktop Linux box for running Freesurfer (and friends), both recon-all, and the interactive graphical tools. I have read the generic recommendations here: http://surfer.nmr.mgh.harvard.edu/fswiki/SystemRequirements (also here as surfer is down)... http://webcache.googleusercontent.com/search?q=cache:Q113A-rSkxEJ:surfer.nm… Feel free to point me to existing email threads if I've missed the place where this was definitively covered! I'd like any more detailed input such as: CPU: Intel vs AMD, and the extent to which more cores increase performance. Video card: -- AMD/ATI or nVidia? My model is that nVidia has had better support for OpenGL/Mesa -- still true? -- if nVidia, then how many CUDA cores and RAM is beneficial for FS's CUDA code? Hard drive: Does SSD make much difference while running recon-all? Linux distro: Which are favored for use with Freesurfer, FSL, etc? Thanks! -- Graham

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convert phillips PAr/Rec files
by Jon Wieser 25 Apr '13

25 Apr '13

dear FS experts I have some PAR/REc format anatomical file from a Phillips scanner. I want to convert the to nifti or MGZ format for freesurfer. how do I do this conversion what program do I use? Jon -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219

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mri_glmfit --no-sim error: cannot find any csd files
by Jeni Chen 24 Apr '13

24 Apr '13

Hello, I was trying to run mri_glmfit-sim at a lower cwpvalthresh so I specified the --no-sim option to avoid re-running the entire simulation again. I entered my DSC file but in the end I get the error message: "cannot find any csd files". Here is what I entered: mri_glmfit-sim \ --glmdir GLMFIT/LH_1GroupAvg_ModVAS_nuissanceAGE_DOSS \ --cwpvalthresh .999 \ --no-sim GLMFIT/LH_1GroupAvg_ModVAS_nuissanceAGE_DOSS/csd/mc-z.abs.3.j001-1GroupAvg-Cor-thickness-Mod-VAS.csd I copied and pasted the csd file from its own folder to the top directory, but it gave the same error. I've attached the error log in case you want to have a look. Thanks for your help! Jeni

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surfer.nmr.mgh.harvard.edu down?
by Graham Wideman 24 Apr '13

24 Apr '13

Hi MGH-ers, >From where I sit (San Diego), http://surfer.nmr.mgh.harvard.edu/ seems to have been non-responsive at least since about 4 pm west-coast time. It's now 4:40 pm. http://nmr.mgh.harvard.edu is working fine. Perhaps you are already on top of this, but in case not... Thanks, -- Graham

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Re: [Freesurfer] Fwd: Conversion
by Douglas N Greve 24 Apr '13

24 Apr '13

This looks wrong: W = TalXFM * Norig * inv(Torig); If RAS = A.vox2ras1 * [i;j;k;1]; (Note: vox2ras = Norig), then just mni305 = TalXFM*A.vox2ras1 * [i;j;k;1] One way to check is to display the MNI305 and ScannerRAS in the tkmedit control window. Take the RAS from the control window, put it into your formula and see if you the MNI305value. doug On 04/24/2013 12:00 PM, Garikoitz Lerma-Usabiaga wrote: > Hi Doug, > I try to make the question shorter, hopefully you will be able to give > me a hint: > > Do you think this method to cut every subjects hippo-subfield > according to their MNI305 Y coordinate could be accurate? > > (for every voxel in every subfield for every subject, do: ) > > > RAS = A.vox2ras1 * [i;j;k;1]; > > > MNI305 = W * RAS; % W = TalXFM * Norig * inv(Torig); > > > if MNI305(2) < -20 then A.vol(i,j,k) = 0; > > > I find that every subject is cut very differently (the Y plane goes > usually to the head), where do you think could be the error, in the > within subject vox2ras or in the MNI305 transformation? Shouldn't I > use this method at all? > > > many many thanks again, > Gari > > > ---------- Forwarded message ---------- > From: *Garikoitz Lerma-Usabiaga* <garikoitz(a)gmail.com > <mailto:garikoitz@gmail.com>> > Date: Sat, Apr 20, 2013 at 2:31 AM > Subject: Conversion > To: Douglas N Greve <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > > Hi Doug, > sorry to bother you again with a direct message, one of your > colleagues has been helping out but I don't think he got it right and > before posting it publicly I would like to know your opinion. > > *OBJECTIVE*: > I want to cut hippo-subfields with a vertical plane in Y. That plane > is defined by a MNI305 coordinate (Y = -20). > > > *METHOD*: > I created a script in Matlab that reads (per every subject): > > TalXFM = xfm_read('talairach.xfm'); > > ORIG = MRIread('orig.mgz'); > > Norig = ORIG.vox2ras; > > Torig = ORIG.tkrvox2ras; > > W = TalXFM * Norig * inv(Torig); > > And reads every hippo_subfield: > > A = MRIread('posterior_left_CA1.mgz'); > > A.vol=permute(A.vol,[2 1 3]); > > Then I just loop through every voxel to set to zero all voxels one > side of that MNI305 coordinate: > > > RAS = A.vox2ras1 * [i;j;k;1]; > > > MNI305 = W * RAS; > > > if MNI305(2) < -20 then A.vol(i,j,k) = 0; > > Then I permute and write it again (afterwards I can sum the modified > volumes per every subfield). > > > A.vol=permute(A.vol,[2 1 3]); > > > MRIwrite(A, 'new_posterior_left_CA1.mgz'); > > > *PROBLEM*: > the vertical plane is not ok, usually it goes out of the hippocampus > or just touches a bit of it (it should separate the head, so be a > quarter of it). But it is a vertical plane. > > > *QUESTIONS*: > > RAS = A.vox2ras1 * [i;j;k;1]; >> Is this Scanner_RAS or Volume_RAS? > > In any case, it gives wrong results (when I compare to freeview or > tkmedit), is this method of calculating RAS coordinates ok? Is there > any other method? > > MNI305 = W * RAS; >> What RAS coordinate should I use here? The > obtained in the previous step is OK? > > Do you think that these methods are accurate enough to accomplish > what I am trying to do or I should try another approach? > > > > Many many thanks again for your help, I will be happy to make the > results available for everybody if this works (I think this makes the > second Samuel Adams :) ) > br, > Gari > > -- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] Fwd: Comparing HRF undershoots between conditions
by Douglas N Greve 24 Apr '13

24 Apr '13

You don't generate a negative coefficient. The sign and magnitude of the coefficient is determined by the fitting procedure. It may be the case that a positive coef fits the data better than a negative. You should not change the gamma parameters. doug On 04/24/2013 04:06 PM, SHAHIN NASR wrote: > > I know but how can we generate negative coefficient? To clarify, we > use alpha=2, delta=2.25 tau=1.25 to generate default HRF. Using > negative values for alpha, delta or tau, does not invert the shape of > the curve (HRF). > > > On Wed, Apr 24, 2013 at 3:12 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > What do you mean the gamma function generates positive values? It > will create a regressor with a positive-going HRF. However, the > regression coefficient can be negative which would invert the > shape. The reg coef is fit to the data, so the data will tell you > whether there is an undershoot or not. > doug > > > > On 04/24/2013 03:02 PM, SHAHIN NASR wrote: > > Hi Doug, > Sorry to follow this topic with a delay but we tried to > model BOLD signal undershoot with a gamma function and we > failed. The problem is, gamma function generates positive > values and we can NOT use "inverse gamma function" (or > otherfunction similar to that) as a part of mkanalysis-sess > (for modeling BOLD signal undershoot). We even used matlab > gammafit to estimate parameters and it said that values should > be positive otherwise gammafit function fails. > Do you have any suggestion? > > > > On Wed, Apr 10, 2013 at 6:46 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: > > > yes, that is what you want. The only other way that comes > to mind > is to model each event type as two event types one delayed > relative to the other. Then model the responseto each as a > gamma. > If the delay is right, then the first gamma should model > the main > positive response and the second gamma will model the negative > response. both will be independent from the other. > > doug > > > On 04/10/2013 05:00 PM, shahin(a)nmr.mgh.harvard.edu > <mailto:shahin@nmr.mgh.harvard.edu> > <mailto:shahin@nmr.mgh.harvard.edu > <mailto:shahin@nmr.mgh.harvard.edu>> wrote: > > I think I figured it out but I want to double check. I am > generating > group-average map for my subjects using isxconcat-sess > command > which > generates ces maps for each time frame. I think these > maps are > what I > wanted. Right? > If you still have other solutions that you think may > generate more > reliable results, I am eager to know. For instance, is > there > anyway to > fit a model as we do for spmhrf or fslhrf, but just > for the > negative > peak? > > Regards > > That's the problem Doug. I have already generated > the FIR > model but how > can > I show the sig MAP for one "particulat time > point". What > are the other > ways? > > > On Wed, Apr 10, 2013 at 4:05 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 Shahin, there are several ways that you > could do > it. The one that > immediately comes to mind is to use an FIR and > then > test for a > difference > at a particular post stimulus time point. > doug > > > > > On 04/10/2013 03:54 PM, SHAHIN NASR wrote: > > Hi, > I want to generate a map to show the > significant difference > between > HRF undershoot (negative peak of activity) > between two conditions > independent from the positive peak. Is there > anyway, to generate this > map? > > P.S.: Please note that I need a map and > not a time > course graph. > > > -- > Shahin Nasr > > PhD in Cognitive Neuroscience > Martinos Imaging Center, MGH > Harvard Medical School > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: > surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting> > > <http://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> > > <http://www.nmr.mgh.harvard.edu/**facility/filedrop/index.html><http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > Outgoing: > ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** > greve/ > > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > > > > > -- > Shahin Nasr > > PhD in Cognitive Neuroscience > Martinos Imaging Center, MGH > Harvard Medical School > > > > -- > Shahin Nasr > > PhD in Cognitive Neuroscience > Martinos Imaging Center, MGH > Harvard Medical School > _______________________________________________ > 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 > > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://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> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > > > -- > Shahin Nasr > > PhD in Cognitive Neuroscience > Martinos Imaging Center, MGH > Harvard Medical School > > > -- > 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: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > > > -- > Shahin Nasr > > PhD in Cognitive Neuroscience > Martinos Imaging Center, MGH > Harvard Medical School -- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Fwd: Comparing HRF undershoots between conditions
by SHAHIN NASR 24 Apr '13

24 Apr '13

That's the problem Doug. I have already generated the FIR model but how can I show the sig MAP for one "particulat time point". What are the other ways? On Wed, Apr 10, 2013 at 4:05 PM, Douglas N Greve <greve(a)nmr.mgh.harvard.edu>wrote: > Hi Shahin, there are several ways that you could do it. The one that > immediately comes to mind is to use an FIR and then test for a difference > at a particular post stimulus time point. > doug > > > > > On 04/10/2013 03:54 PM, SHAHIN NASR wrote: > >> Hi, >> I want to generate a map to show the significant difference between >> HRF undershoot (negative peak of activity) between two conditions >> independent from the positive peak. Is there anyway, to generate this map? >> >> P.S.: Please note that I need a map and not a time course graph. >> >> >> -- >> Shahin Nasr >> >> PhD in Cognitive Neuroscience >> Martinos Imaging Center, MGH >> Harvard Medical School >> > > -- > 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<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> > Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** > greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > > > -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School

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