Re: [Freesurfer] Rat template creation: MRIstripskull failed
Hi, Ok, I will look into inverting the image as Martin suggested. Is there some background info available on how to put the segmentation input into the surface-based analysis. In case the inversion doesn't work. I'm particularly wondering if I need to have the images in *.mgz file format or would nifti or something of that sort suffice? Thanks Mark Bruce Fischl wrote: Hi Mark, if wm is darker than gm our tools probably will not work. You might try using the FSL segmentation tools and putting the output of them through our stream for surface-based analysis. cheers, Bruce On Mon, 20 Oct 2008, Mark Bouts wrote: Hi, I'm trying to set up a rat brain template for analysis using the freesurfer tool. Before setting up the complete template I have to process a representable rat dataset with the available human template. With some much appreciated help I managed to get to the skull strip procedure . But the application ceases its operations at this point with the message: White matter intensity 0 is lower than CSF intensity 21. Please examine input images. Will terminate ... Evaluation using tkmedit does not show something a proper segmentation of the rat brain, however it does show a proper outline of the brain. Since a rat brain and a human brain are very dissimilar I'm not surprised by the fact that the segmentation is incorrect. However the brain is outlined ok. It is also known that the WM intensity values in the rat dataset is somewhat reduced to the GM structure. Which is not expected by the freesurfer tool, which expects WM to be highest intensity value. My question is: is there a way of circumventing this problem. For instance by defining the mean intensity values of each tissue class or.. Hope someone can help me? Thanks! Mark ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mesh size question
Thank you Martin, I only wanted know if there is a way to do this without using an external program. I will try using a standard tool. Tommaso Martin Reuter wrote: Hi Tommaso, I am not sure about freesurfer, but why don't you simply use a standard tool for mesh simplification e.g. qslim http://graphics.cs.uiuc.edu/~garland/software/qslim.html probably there are more. Martin On Wed, 2008-10-22 at 14:48 +0200, Tommaso De Marco wrote: Hi all, I'm using the mri_watershed instruction to extract the skull and skin mesh, because I'm using them in a boundary element method, but the dimensions of these meshes are too big for my application (20480 faces and 10242 vertices for each ones). Do you know if there is a way to define a maximum mesh size for the mri_watershed instruction (or at least an equivalent instruction in which is possible to do it) ? I need of very coarse meshes ( 1000 faces for each ones for example). Thanks! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Error with mri_convert failing to write orig/001.mgz
Hey Krish, Thanks for your input. Good idea too, never thought about doing that. Tried this in command line and worked without a hitch. Then i realized if you just use command line what I did before works as well. The error must somehow be resulting from issues with tcsh or something. But I found a way to get it to work in tcsh shell script, going off of what you suggested. Here is what works for me in tcsh script: cd $FSsubjDir mkdir $subjID cd $subjID mkdir mri cd mri mkdir orig cd orig mv ../../Volume_ns+orig* ./ mri_convert --in_type brik Volume_ns+orig.BRIK 001.mgz etc etc That's probably a primitive way to write the script, but hey, it works. Thanks for the help! John On Wed, Oct 22, 2008 at 10:34 PM, Krish Subramaniam [EMAIL PROTECTED] wrote: John Is orig/ already there ? Otherwise try mkdir orig mri_convert --in_type brik Volume_ns+orig.BRIK 001.mgz mv 001.mgz orig/ Thanks Krish On Oct 22, 2008, at 10:01 PM, John Sheppard wrote: Hey everyone, I'm having some issues trying to run the volume pipeline using .BRIK input from afni (hence running mri_convert command directly). The problem occurs at the end of mri_convert at the very beginning when Freesurfer fails to write orig/001.mgz, and I'm not sure if I'm making a mistake without realizing it or if something weirder is going on. I've tried this on both a Mac and a linux station running RHEL, with the same results. I ran the script using sudo in RHEL so I do not think this is a permissions issue. The error occurs right when it tries to write orig/001.mgz: writing to orig/001.mgz... sh: orig/001.mgz: No such file or directory Broken pipe I'm not really familiar with working with pipes but I'm guessing I shouldn't have to deal with that. Just curious if anyone has encoutered this before and knows what's going on. Didn't find this issue in prior mailing list emails, so I hope this isn't a repeat question. Thanks! John Sheppard Recon output below: mri_convert --in_type brik Volume_ns+orig.BRIK orig/001.mgz $Id: mri_convert.c,v 1.146.2.3 2008/08/11 22:18:58 nicks Exp $ reading from Volume_ns+orig.BRIK... AFNI Header Information DATASET_RANK : spatial dims 3, sub-bricks 1 DATASET_DIMENSIONS: (256, 256, 160) TYPESTRING: 3DIM_HEAD_ANAT SCENE_DATA: view type 0, func type 0, verify 0 ORIGIN: (-172.926697, 84.177513, -82.874474) DELTA : (1.00, -1.00, 1.00) IDCODE_STRING : XYZ_FSWwmSca-raNtz0oRbtKow BYTEORDER_STRING : LSB_FIRST BRICK_STATS : min 0.00 max 950.00 BRICK_TYPES : short BRICK_FLOAT_FACS : 0.00 BRICK_STATS min = 0.00 -- actual min = 0.00 BRICK_STATS max = 950.00 -- actual max = 950.00 TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0, -1, 0) j_ras = (0, 0, -1) k_ras = (-1, 0, 0) writing to orig/001.mgz... sh: orig/001.mgz: No such file or directory Broken pipe Subject Stamp: freesurfer-Linux-centos4-stable-pub-v4.1.0 Current Stamp: freesurfer-Linux-centos4-stable-pub-v4.1.0 INFO: SUBJECTS_DIR is /mnt/win/MTLD1/autorecon Actual FREESURFER_HOME /usr/local/freesurfer Linux SLR10.soc.northwestern.edu 2.6.18-92.1.13.el5 #1 SMP Thu Sep 4 03:51:01 EDT 2008 i686 i686 i386 GNU/Linux # [EMAIL PROTECTED] MotionCor Wed Oct 22 20:45:32 CDT 2008 ERROR: no run data found in /mnt/win/MTLD1/autorecon/E-05-010-2-afni-test/mri. Make sure to have a volume called 001.mgz in /mnt/win/MTLD1/autorecon/E-05-010-2-afni-test/mri/orig. -- John Sheppard Undergraduate Student (Class of 2010) Department of Biomedical Engineering Northwestern University Phone: (630) 957-8321 E-mail: [EMAIL PROTECTED] Address: 1927 Orrington Ave. Rm 8203 Evanston, IL 60201 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- John Sheppard Undergraduate Student (Class of 2010) Department of Biomedical Engineering Northwestern University Phone: (630) 957-8321 E-mail: [EMAIL PROTECTED] Address: 1927 Orrington Ave. Rm 8203 Evanston, IL 60201 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Error with mri_convert failing to write orig/001.mgz
Also, in case anyone is interested -- if you have a brik volume in the subject folder, specifying mri/orig/001.mgz gives the same error as specifying orig/001.mgz, at least for me. So that wasn't the cause of the problem. John On Thu, Oct 23, 2008 at 7:44 AM, John Sheppard [EMAIL PROTECTED] wrote: Hey Krish, Thanks for your input. Good idea too, never thought about doing that. Tried this in command line and worked without a hitch. Then i realized if you just use command line what I did before works as well. The error must somehow be resulting from issues with tcsh or something. But I found a way to get it to work in tcsh shell script, going off of what you suggested. Here is what works for me in tcsh script: cd $FSsubjDir mkdir $subjID cd $subjID mkdir mri cd mri mkdir orig cd orig mv ../../Volume_ns+orig* ./ mri_convert --in_type brik Volume_ns+orig.BRIK 001.mgz etc etc That's probably a primitive way to write the script, but hey, it works. Thanks for the help! John On Wed, Oct 22, 2008 at 10:34 PM, Krish Subramaniam [EMAIL PROTECTED] wrote: John Is orig/ already there ? Otherwise try mkdir orig mri_convert --in_type brik Volume_ns+orig.BRIK 001.mgz mv 001.mgz orig/ Thanks Krish On Oct 22, 2008, at 10:01 PM, John Sheppard wrote: Hey everyone, I'm having some issues trying to run the volume pipeline using .BRIK input from afni (hence running mri_convert command directly). The problem occurs at the end of mri_convert at the very beginning when Freesurfer fails to write orig/001.mgz, and I'm not sure if I'm making a mistake without realizing it or if something weirder is going on. I've tried this on both a Mac and a linux station running RHEL, with the same results. I ran the script using sudo in RHEL so I do not think this is a permissions issue. The error occurs right when it tries to write orig/001.mgz: writing to orig/001.mgz... sh: orig/001.mgz: No such file or directory Broken pipe I'm not really familiar with working with pipes but I'm guessing I shouldn't have to deal with that. Just curious if anyone has encoutered this before and knows what's going on. Didn't find this issue in prior mailing list emails, so I hope this isn't a repeat question. Thanks! John Sheppard Recon output below: mri_convert --in_type brik Volume_ns+orig.BRIK orig/001.mgz $Id: mri_convert.c,v 1.146.2.3 2008/08/11 22:18:58 nicks Exp $ reading from Volume_ns+orig.BRIK... AFNI Header Information DATASET_RANK : spatial dims 3, sub-bricks 1 DATASET_DIMENSIONS: (256, 256, 160) TYPESTRING: 3DIM_HEAD_ANAT SCENE_DATA: view type 0, func type 0, verify 0 ORIGIN: (-172.926697, 84.177513, -82.874474) DELTA : (1.00, -1.00, 1.00) IDCODE_STRING : XYZ_FSWwmSca-raNtz0oRbtKow BYTEORDER_STRING : LSB_FIRST BRICK_STATS : min 0.00 max 950.00 BRICK_TYPES : short BRICK_FLOAT_FACS : 0.00 BRICK_STATS min = 0.00 -- actual min = 0.00 BRICK_STATS max = 950.00 -- actual max = 950.00 TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0, -1, 0) j_ras = (0, 0, -1) k_ras = (-1, 0, 0) writing to orig/001.mgz... sh: orig/001.mgz: No such file or directory Broken pipe Subject Stamp: freesurfer-Linux-centos4-stable-pub-v4.1.0 Current Stamp: freesurfer-Linux-centos4-stable-pub-v4.1.0 INFO: SUBJECTS_DIR is /mnt/win/MTLD1/autorecon Actual FREESURFER_HOME /usr/local/freesurfer Linux SLR10.soc.northwestern.edu 2.6.18-92.1.13.el5 #1 SMP Thu Sep 4 03:51:01 EDT 2008 i686 i686 i386 GNU/Linux # [EMAIL PROTECTED] MotionCor Wed Oct 22 20:45:32 CDT 2008 ERROR: no run data found in /mnt/win/MTLD1/autorecon/E-05-010-2-afni-test/mri. Make sure to have a volume called 001.mgz in /mnt/win/MTLD1/autorecon/E-05-010-2-afni-test/mri/orig. -- John Sheppard Undergraduate Student (Class of 2010) Department of Biomedical Engineering Northwestern University Phone: (630) 957-8321 E-mail: [EMAIL PROTECTED] Address: 1927 Orrington Ave. Rm 8203 Evanston, IL 60201 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- John Sheppard Undergraduate Student (Class of 2010) Department of Biomedical Engineering Northwestern University Phone: (630) 957-8321 E-mail: [EMAIL PROTECTED] Address: 1927 Orrington Ave. Rm 8203 Evanston, IL 60201 -- John Sheppard Undergraduate Student (Class of 2010) Department of Biomedical Engineering Northwestern University Phone: (630) 957-8321 E-mail: [EMAIL PROTECTED] Address: 1927 Orrington Ave. Rm 8203 Evanston, IL 60201 ___ Freesurfer mailing list
Re: [Freesurfer] questions about longitudinal analysis
Hi Wang, 1. An affine transform from tp1 to tp2 would only remove global atrophy, but not the region effects we are interested in. 2. For intra-subject registration the surface-based is not needed as we expect the changes to be small. cheers, Bruce On Thu, 23 Oct 2008, Wang, Xin wrote: Hi, groups, I noticed the updates of longitudinal analysis in the new version of Freesurfer. However, I still have a couple of questions about the goal of longitudinal analysis. 1. The goal of longitudinal analysis is to detect the atrophy (thinning), but the transformation in the registration step will minimize any atrophy. An example of outcomes of FLIRT and FNIRT on FSL website exactly demonstrates that the atrophy disappears in the 'best' transformation (FNIRT) http://www.fmrib.ox.ac.uk/fsl/fnirt/index.html. In our experience, the number of vertex of post-transformed tp2 is very close to tp1. It is not clear to me how the difference in the original thickness between tp2 and tp1 is preserved in this transformation. One may argue that processing tp1 and tp2 independently does not solve this problem because the registration is also used in the routine recon. Is it true? 2. The new longitudinal process is still using volume-based registration if I read it correctly. Why not switch to surface-based since people have argued the advantage of surface-based over volume-based? Thank you for any clarification, Wang ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_convert
mri_convert file.mgz file.img should do the trick (or file.nii for nifti) On Thu, 23 Oct 2008, sameer kumar wrote: Hi Nick, After I run recon-all, the files I get are not in mgz format and I would like to convert them into img format to view them in FSL view. How can I do that? Thanks, Regards, Sameer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] FreeSurferColorLUT aparc
and how do you get it into FSL? On Wed, 22 Oct 2008, Juranek, Jenifer wrote: yes, the correct Sgmtn label is displayed in the TkMedit Tools -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Wednesday, October 22, 2008 4:30 PM To: Juranek, Jenifer Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] FreeSurferColorLUT aparc if you load it in tkmedit is it displayed properly? On Wed, 22 Oct 2008, Juranek, Jenifer wrote: I'm able to view the intensity values in FSL. Is there another approach I can take to doublecheck? Jenifer -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Wednesday, October 22, 2008 4:15 PM To: Juranek, Jenifer Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FreeSurferColorLUT aparc Hi Jenifer, how are you getting those intensity values? Bruce On Wed, 22 Oct 2008, Juranek, Jenifer wrote: Hi, Running fsv405 on RHEL5. I've encountered some unexpected numerical values wrt FreeSurferColorLUT.txt. Are my expectations off? 1) In the aparc+aseg.mgz file, intensity values for the cortical labels range from -32768 to 654, with negative values falling in some regions in the left hemisphere. 2) Identical results are obtained if mri_aparc2aseg is used to generate an output file: mri_aparc2aseg --s mysubject --o ./aparc2aseg.mgz 3) Values of aseg.mgz map perfectly well to FreeSurferColorLUT.txt Example values obtained from aparc+aseg.mgz are listed below: lh.superiortemporal=484 (expecting 1030 from FreeSurferColorLUT.txt) rh.superiortemporal=32767 (expecting 2030) Although these numerical values do not match the LUT, they are consistent across subjects. Many Thanks for any insights... Jenifer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_convert
Hi all, It says .mgz file not found. I am new to FS so please help me out with this. Thanks, Regards, Sameer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_convert
what file are you trying to convert? On Thu, 23 Oct 2008, sameer kumar wrote: Hi all, It says .mgz file not found. I am new to FS so please help me out with this. Thanks, Regards, Sameer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_convert
The output files of recon-all ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_convert
which ones? There are many, some of them are surfaces, which I don't think FSL can show, and some are volume that you could import into FSL (e.g. $SUBJECTS_DIR/$subject/mri/aseg.mgz, which is the whole-brain segmentation) cheers, Bruce On Thu, 23 Oct 2008, sameer kumar wrote: The output files of recon-all ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] creating intermediate surfaces
Hi all - Is there a way to create intermediate surfaces in FreeSurfer? By intermediate I mean some fraction between gray/white and pial. Cheers -=R -- Rudolph Pienaar, M.Eng, D.Eng / email: [EMAIL PROTECTED] MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street, Charlestown, MA 02129 USA ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] creating intermediate surfaces
yes, mris_expand will do it. cheers Bruce On Thu, 23 Oct 2008, Rudolph Pienaar wrote: Hi all - Is there a way to create intermediate surfaces in FreeSurfer? By intermediate I mean some fraction between gray/white and pial. Cheers -=R ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Bug with aparcstats2table on aparc.a2005s parcellation
Hello, Not sure if this bug has been mentioned before, but there is a bug with using aparcstats2table for the aparc.a2005s parcellation map. If some of the subjects in the group have missing values of a certain type, aparcstats2table fails to designate a 0 for them. So for instance, it's often the case that a subject has no lh_unknown_volume in their aparc.a2005s.stats. Certain other, seemingly random areas will fail to print out as well. This will lead to shifts in the dataset, so that every volume after the missing value for a subject will be incorrect, and will need to be shifted for the blank. The only way I have found to reliably check that the data is valid is to generate seperate stats tables for each subject. Anyway, this is a serious problem for people who collect and analyse data with aparcstats2table using the aparc.a2005s parcellation map. Attached are two examples illustrating the problem. To make it clearer, paste the contents of both into excel, and look at the column mismatch; some of the subjects' data don't make it all the way to the end, and a shift in the values is clear. Victor Laluz : Imaging Coordinator : UCSF Memory and Aging Center 415-476-1680 : 415-476-1816 (fax) lh.aparc.a2005s.volume lh_G_cingulate-Isthmus_volume lh_G_cingulate-Main_part_volume lh_G_cuneus_volume lh_G_frontal_inf-Opercular_part_volume lh_G_frontal_inf-Orbital_part_volume lh_G_frontal_inf-Triangular_part_volume lh_G_frontal_middle_volume lh_G_frontal_superior_volume lh_G_frontomarginal_volume lh_G_insular_long_volume lh_G_insular_short_volume lh_G_and_S_occipital_inferior_volume lh_G_occipital_middle_volume lh_G_occipital_superior_volume lh_G_occipit-temp_lat-Or_fusiform_volume lh_G_occipit-temp_med-Lingual_part_volume lh_G_occipit-temp_med-Parahippocampal_part_volume lh_G_orbital_volume lh_G_paracentral_volume lh_G_parietal_inferior-Angular_part_volume lh_G_parietal_inferior-Supramarginal_part_volume lh_G_parietal_superior_volume lh_G_postcentral_volume lh_G_precentral_volume lh_G_precuneus_volume lh_G_rectus_volume lh_G_subcallosal_volume lh_G_subcentral_volume lh_G_temporal_inferior_volume lh_G_temporal_middle_volume lh_G_temp_sup-G_temp_transv_and_interm_S_volume lh_G_temp_sup-Lateral_aspect_volume lh_G_temp_sup-Planum_polare_volume lh_G_temp_sup-Planum_tempolare_volume lh_G_and_S_transverse_frontopolar_volume lh_Lat_Fissure-ant_sgt-ramus_horizontal_volume lh_Lat_Fissure-ant_sgt-ramus_vertical_volume lh_Lat_Fissure-post_sgt_volume lh_Medial_wall_volume lh_Pole_occipital_volume lh_Pole_temporal_volume lh_S_calcarine_volume lh_S_central_volume lh_S_central_insula_volume lh_S_cingulate-Main_part_and_Intracingulate_volume lh_S_cingulate-Marginalis_part_volume lh_S_circular_insula_anterior_volume lh_S_circular_insula_inferior_volume lh_S_circular_insula_superior_volume lh_S_collateral_transverse_ant_volume lh_S_collateral_transverse_post_volume lh_S_frontal_inferior_volume lh_S_frontal_middle_volume lh_S_frontal_superior_volume lh_S_frontomarginal_volume lh_S_intermedius_primus-Jensen_volume lh_S_intraparietal-and_Parietal_transverse_volume lh_S_occipital_anterior_volume lh_S_occipital_middle_and_Lunatus_volume lh_S_occipital_superior_and_transversalis_volume lh_S_occipito-temporal_lateral_volume lh_S_occipito-temporal_medial_and_S_Lingual_volume lh_S_orbital-H_shapped_volume lh_S_orbital_lateral_volume lh_S_orbital_medial-Or_olfactory_volume lh_S_paracentral_volume lh_S_parieto_occipital_volume lh_S_pericallosal_volume lh_S_postcentral_volume lh_S_precentral-Inferior-part_volume lh_S_precentral-Superior-part_volume lh_S_subcentral_ant_volume lh_S_subcentral_post_volume lh_S_suborbital_volume lh_S_subparietal_volume lh_S_temporal_inferior_volume lh_S_temporal_superior_volume lh_S_temporal_transverse_volume SCAN-1 642 4032 2086 3330 782 2155 7916 19741 1074 888 1796 2673 4789 3052 2833 4670 4548 5530 2060 6433 6555 5232 4639 5662 5372 1865 577 2342 8379 9405 1262 5386 1569 1986 1579 460 379 1414 5046 3724 4569 3614 3399 295 6836 1115 1007 2680 2922 1229 380 2456 3542 4848 1001 577 4293 1168 1773 1704 1538 3604 2930 454 1152 275 2820 1068 5991 1959 2586 97 618 1183 1718 2590 9959 449 SCAN-2 321 4083 2477 3438 737 2980 7537 18220 828 1210 1671 3567 4352 2262 4642 3483 3599 5848 2996 5078 7150 4910 3587 6080 4388 2268 640 2208 5962 6908 1039 5437 1386 1503 1719 320 585 1496 4758 3606 5182 2065 4092 295 6798 1486 964 2055 2202 1156 667 3096 2952 4933 846 1619 3760 1290 1095 1093 967 3275 2308 884 1038 529 2398 1255 3285 1995 2863 169 425 903 1312 1283 6625 421 SCAN-3 515 5007 3321 2835 624 2466 8741 16566 956 1085 1574 3668 4699 3259 3482 5243 4777 6510 2156 7038 5367 7198 4501 5395 6090 2279 334 2298 7256 8527 877 6448 1703 1465 2177 487 309 1314 6394 3600 5203 2653 3327 436 6525 1339 885 1796 2606 1754 580 4233 1336 3206 1227 265 4289 1163 1891 1867 1392 3731 2679 537 814 133 2745 1245 4294 1963 1795 14 541 1162 1548 2008 9924 302 SCAN-4 1571 152
[Freesurfer] optseq psdwin
Hi, I have 2 questions. 1) How do I calculate psd min, max, and dpsd. Is there a formula for calculating these values? I have 4 kinds of stimuli, stim duration = 3s, stim repetition = 25, TR =2 so: optseq2 --ntp 180 --tr 2 --psdwin [?] --ev A 3 25 --ev B 3 25 --ev C 3 25 --ev D 3 25 --o 4types --tsearch 10 --nkeep 4 What should my psd min, max, and dpsd be? 2) My task is history-dependent. I would like to control the probabilities that stimulus B follows A, C follows A, A follows D... Is there a way for me to do that with optseq? Thank you so much for your help. Cheers, Linh ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] convert multiple Analyze to single 4D nifti
Does anybody know how to convert a series of Analyze files into a single nii file? Each analyze file is a single 3D volume at a time point; the nii file would be 4d. Thanks, Xu -- Xu Cui Department of Psychiatry and Behavioral Sciences Stanford University ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Bug with aparcstats2table on aparc.a2005s parcellation - addendum
The body of my email was lost because of the attachments: here it is again for those who are curious. Sorry about that, I didn't know a text file attachment would do that. Not sure if this bug has been mentioned before, but there is a bug with using aparcstats2table for the aparc.a2005s parcellation map. If some of the subjects in the group have missing values of a certain type, aparcstats2table fails to designate a 0 for them. So for instance, it's often the case that a subject has no lh_unknown_volume in their aparc.a2005s.stats. Certain other, seemingly random areas will fail to print out as well. This will lead to shifts in the dataset, so that every volume after the missing value for a subject will be incorrect, and will need to be shifted for the blank. The only way I have found to reliably check that the data is valid is to generate seperate stats tables for each subject. Anyway, this is a serious problem for people who collect and analyse data with aparcstats2table using the aparc.a2005s parcellation map. Attached are two examples illustrating the problem. To make it clearer, paste the contents of both into excel, and look at the column mismatch; some of the subjects' data don't make it all the way to the end, and a shift in the values is clear. Victor Laluz : Imaging Coordinator : UCSF Memory and Aging Center 415-476-1680 : 415-476-1816 (fax) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Bug with aparcstats2table on aparc.a2005s parcellation - addendum
Victor, We are aware of this bug. Unfortunately, there is no 'quick fix', which is why it has not been repaired yet. But yes, I agree its an ugly one which creates havoc with automated scripts. Hopefully a fix will appear in the next release. Nick On Thu, 2008-10-23 at 13:19 -0700, Laluz, Victor wrote: The body of my email was lost because of the attachments: here it is again for those who are curious. Sorry about that, I didn’t know a text file attachment would do that. Not sure if this bug has been mentioned before, but there is a bug with using aparcstats2table for the aparc.a2005s parcellation map. If some of the subjects in the group have missing values of a certain type, aparcstats2table fails to designate a 0 for them. So for instance, it’s often the case that a subject has no lh_unknown_volume in their aparc.a2005s.stats. Certain other, seemingly random areas will fail to print out as well. This will lead to shifts in the dataset, so that every volume after the missing value for a subject will be incorrect, and will need to be shifted for the blank. The only way I have found to reliably check that the data is valid is to generate seperate stats tables for each subject. Anyway, this is a serious problem for people who collect and analyse data with aparcstats2table using the aparc.a2005s parcellation map. Attached are two examples illustrating the problem. To make it clearer, paste the contents of both into excel, and look at the column mismatch; some of the subjects’ data don’t make it all the way to the end, and a shift in the values is clear. Victor Laluz : Imaging Coordinator : UCSF Memory and Aging Center 415-476-1680 : 415-476-1816 (fax) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
